A few questions:
Does your app force people to upgrade? Or allow them to keep running old versions?
When did you implement the campaign tracking? Could it be that the second app isn't updated? (If yes to the question above, is it possible that the click is being tracked because it's a new enough version, but the second app hasn't been updated and doesn't have the tracking in place?)
Is it possible, in the Android case, that the users don't have the second app installed? And therefore the click is registered, but there is no corresponding app to capture the incoming traffic?
For iOS (more incoming than outgoing clicks)... Is it possible that the campaign tracking is being tracked on both the lifecycle call and the first page (causing multiple tracking for one incoming referral?) Or, I've seen instances in our own app where the page "loads twice" causing duplicate tracking... when the app was opened via a deep link... I had to get our developers to fix that in our case.
Have you run the integrated scenario through rigorous testing to see if you can spot any issues?
These are just a few scenarios that come to mind, there may be others that I haven't yet considered....