*ERROR* [OsgiInstallerImpl] Cannot register Component (java.lang.IllegalStateException: Invalid BundleContext.)

Is the status of the component is 'Active' ?? 

From your description assuming it is interment & does not affect any functionality.

The error indicates there is another process in the middle of using the BundleContext and other thread trying to stops the bundle, hence the BundleContext will become invalid. Complete logs could give better picture or you can find yourself by analyzing what is happening in parallel. 

BTB which aem version you are using?  Because "Cannot register Component" should provide complete strack trace OR did you truncated?

I am running AEM 5.6.1

Since some of the components are active and some other are registered, I am not sure if component status = active is the issue (it seems like the root problem occurred before the components are loaded by OSGi).

active:
com.tcm.core.ReplicationLogger
com.tcm.core.components.ModifyPermissions

registered:
com.tcm.core.StockDataImporter
com.tcm.core.servlets.SearchServlet
com.tcm.core.components.StockAlertProcess

My only     @Reference are out of the box sling components as per below, which I confirmed showed correctly from the system console.

    @Reference
    private SlingRepository repo;

http://localhost:4502/system/console/bundles/324
Imported Packages
org.apache.sling.jcr.api,version=2.1.0 from org.apache.sling.jcr.api (74)

http://localhost:4502/system/console/services/141
org.apache.sling.jcr.api.SlingRepository]

    @Reference
    private Scheduler scheduler;

http://localhost:4502/system/console/services/132
org.apache.sling.commons.scheduler,version=2.2.0 from org.apache.sling.commons.scheduler (132)

I might have Intellij IDEA open with a Maven bundle build (not running when AEM started up); other than that I do not have any AEM bundle related applications running.

The log entries are numerous; but I have included the log entries leading up to the error.

21.07.2014 09:37:43.354 *INFO* [OsgiInstallerImpl] org.apache.sling.servlets.resolver.internal.resource.ServletResourceProviderFactory create(2585): ServiceReference has no registration settings, ignoring
21.07.2014 09:37:43.354 *INFO* [OsgiInstallerImpl] org.apache.felix.inventory Service [2584] ServiceEvent REGISTERED
21.07.2014 09:37:43.355 *INFO* [OsgiInstallerImpl] org.apache.sling.scripting.jsp Service [2583] ServiceEvent REGISTERED
21.07.2014 09:37:43.355 *INFO* [OsgiInstallerImpl] org.apache.sling.scripting.jsp Service [JSP Script Modification Handler,2586] ServiceEvent REGISTERED
21.07.2014 09:37:43.356 *INFO* [OsgiInstallerImpl] org.apache.sling.scripting.core.impl.ScriptEngineManagerFactory Adding ScriptEngine Apache Sling JST script engine (Sling JavaScript Templates), 1.0 for language JavaScript Templates, 1.0
21.07.2014 09:37:43.356 *INFO* [OsgiInstallerImpl] org.apache.sling.scripting.core.impl.ScriptEngineManagerFactory Adding ScriptEngine Apache Sling Scripting JavaScript Support (Rhino 1.6 release 6 2007 07 26), 2.0.12 for language ECMAScript, 0
21.07.2014 09:37:43.356 *INFO* [OsgiInstallerImpl] org.apache.sling.scripting.core.impl.ScriptEngineManagerFactory Adding ScriptEngine Apache Sling Scripting Java Support, 2.0.6 for language Java Servlet Compiler, 1.5
21.07.2014 09:37:43.356 *INFO* [OsgiInstallerImpl] org.apache.sling.scripting.core.impl.ScriptEngineManagerFactory Adding ScriptEngine Apache Sling Scripting JSP Support, 2.0.28 for language Java Server Pages, 2.1
21.07.2014 09:37:43.356 *INFO* [OsgiInstallerImpl] org.apache.sling.scripting.core.impl.ScriptEngineManagerFactory Script extension 'ecma' is now handled by ScriptEngine 'Apache Sling Scripting JavaScript Support (Rhino 1.6 release 6 2007 07 26)', version='2.0.12', class='org.apache.sling.scripting.javascript.internal.RhinoJavaScriptEngine'
21.07.2014 09:37:43.357 *INFO* [OsgiInstallerImpl] org.apache.sling.scripting.core.impl.ScriptEngineManagerFactory Script extension 'esp' is now handled by ScriptEngine 'Apache Sling Scripting JavaScript Support (Rhino 1.6 release 6 2007 07 26)', version='2.0.12', class='org.apache.sling.scripting.javascript.internal.RhinoJavaScriptEngine'
21.07.2014 09:37:43.357 *INFO* [OsgiInstallerImpl] org.apache.sling.scripting.core.impl.ScriptEngineManagerFactory Script extension 'java' is now handled by ScriptEngine 'Apache Sling Scripting Java Support', version='2.0.6', class='org.apache.sling.scripting.java.impl.JavaScriptEngineFactory$JavaScriptEngine'
21.07.2014 09:37:43.357 *INFO* [OsgiInstallerImpl] org.apache.sling.scripting.core.impl.ScriptEngineManagerFactory Script extension 'jsp' is now handled by ScriptEngine 'Apache Sling Scripting JSP Support', version='2.0.28', class='org.apache.sling.scripting.jsp.JspScriptEngineFactory$JspScriptEngine'
21.07.2014 09:37:43.357 *INFO* [OsgiInstallerImpl] org.apache.sling.scripting.core.impl.ScriptEngineManagerFactory Script extension 'jspf' is now handled by ScriptEngine 'Apache Sling Scripting JSP Support', version='2.0.28', class='org.apache.sling.scripting.jsp.JspScriptEngineFactory$JspScriptEngine'
21.07.2014 09:37:43.357 *INFO* [OsgiInstallerImpl] org.apache.sling.scripting.core.impl.ScriptEngineManagerFactory Script extension 'jspx' is now handled by ScriptEngine 'Apache Sling Scripting JSP Support', version='2.0.28', class='org.apache.sling.scripting.jsp.JspScriptEngineFactory$JspScriptEngine'
21.07.2014 09:37:43.357 *INFO* [OsgiInstallerImpl] org.apache.sling.scripting.core.impl.ScriptEngineManagerFactory Script extension 'jst' is now handled by ScriptEngine 'Apache Sling JST script engine (Sling JavaScript Templates)', version='1.0', class='org.apache.sling.scripting.jst.JstScriptEngine'
21.07.2014 09:37:43.357 *INFO* [OsgiInstallerImpl] com.tcm.core-bundle BundleEvent UNRESOLVED
21.07.2014 09:37:43.357 *INFO* [OsgiInstallerImpl] com.tcm.core-bundle BundleEvent UPDATED
21.07.2014 09:37:43.386 *INFO* [FelixDispatchQueue] org.apache.felix.framework FrameworkEvent PACKAGES REFRESHED
21.07.2014 09:37:43.386 *INFO* [OsgiInstallerImpl] org.apache.sling.audit.osgi.installer Updated bundle com.tcm.core-bundle [324] from resource TaskResource(url=jcrinstall:/apps/training/install/core-bundle-1.0-SNAPSHOT.jar, entity=bundle:com.tcm.core-bundle, state=INSTALL, attributes=[org.apache.sling.installer.api.tasks.ResourceTransformer=:77:16:, Bundle-SymbolicName=com.tcm.core-bundle, Bundle-Version=1.0.0.SNAPSHOT], digest=1405949861300)
21.07.2014 09:37:43.479 *INFO* [OsgiInstallerImpl] org.apache.sling.audit.osgi.installer Refreshing 1 bundles: [com.tcm.core-bundle [324]]
21.07.2014 09:37:43.479 *INFO* [OsgiInstallerImpl] org.apache.sling.audit.osgi.installer Waiting up to 90 seconds for bundles refresh
21.07.2014 09:37:43.480 *INFO* [OsgiInstallerImpl] org.apache.sling.audit.osgi.installer Done refreshing 1 bundles
21.07.2014 09:37:43.481 *INFO* [FelixDispatchQueue] org.apache.felix.framework FrameworkEvent PACKAGES REFRESHED
21.07.2014 09:37:43.489 *INFO* [OsgiInstallerImpl] com.tcm.core-bundle BundleEvent RESOLVED
21.07.2014 09:37:43.495 *INFO* [OsgiInstallerImpl] com.tcm.core-bundle BundleEvent STARTING
21.07.2014 09:37:43.495 *INFO* [OsgiInstallerImpl] com.tcm.core-bundle BundleEvent STARTED

21.07.2014 09:37:43.498 *ERROR* [OsgiInstallerImpl] com.tcm.core-bundle [com.tcm.core.ReplicationLogger] Cannot register Component (java.lang.IllegalStateException: Invalid BundleContext.) java.lang.IllegalStateException: Invalid BundleContext.
    at org.apache.felix.framework.BundleContextImpl.checkValidity(BundleContextImpl.java:514)
    at org.apache.felix.framework.BundleContextImpl.getBundle(BundleContextImpl.java:112)
    at org.apache.felix.scr.impl.ComponentRegistry.checkComponentName(ComponentRegistry.java:355)
    at org.apache.felix.scr.impl.BundleComponentActivator.loadDescriptor(BundleComponentActivator.java:240)
    at org.apache.felix.scr.impl.BundleComponentActivator.initialize(BundleComponentActivator.java:149)
    at org.apache.felix.scr.impl.BundleComponentActivator.<init>(BundleComponentActivator.java:113)
    at org.apache.felix.scr.impl.Activator.loadComponents(Activator.java:261)
    at org.apache.felix.scr.impl.Activator.bundleChanged(Activator.java:179)
    at org.apache.felix.framework.util.EventDispatcher.invokeBundleListenerCallback(EventDispatcher.java:868)
    at org.apache.felix.framework.util.EventDispatcher.fireEventImmediately(EventDispatcher.java:789)
    at org.apache.felix.framework.util.EventDispatcher.fireBundleEvent(EventDispatcher.java:514)
    at org.apache.felix.framework.Felix.fireBundleEvent(Felix.java:4385)
    at org.apache.felix.framework.Felix.startBundle(Felix.java:2080)
    at org.apache.felix.framework.BundleImpl.start(BundleImpl.java:955)
    at org.apache.felix.framework.BundleImpl.start(BundleImpl.java:942)
    at org.apache.sling.installer.core.impl.tasks.BundleStartTask.execute(BundleStartTask.java:93)
    at org.apache.sling.installer.core.impl.OsgiInstallerImpl.executeTasks(OsgiInstallerImpl.java:733)
    at org.apache.sling.installer.core.impl.OsgiInstallerImpl.run(OsgiInstallerImpl.java:247)
    at java.lang.Thread.run(Unknown Source)

also, what is the status of all the @reference services you have used in your servlet