Thanks everyone for spending sometime for the below issue.
Now we have the root cause of the below warning that is :
We have one org.apache.sling.rewriter.Transformer and org.apache.sling.rewriter.TransformerFactory implementation in our project that was looking for the path, which was deleted as part of the deletion activity, and trying to do some operation.
If the issue is not reproducible on the WKND site, I highly doubt it's an issue with the core AEM code and the issue might be related to the Sling model Or other backend custom code that gets invoked during the component deletion.
That said, If you are able to reproduce it without any custom code, I would recommend logging a support case.