If a warning, suspect application, changed property etc is reported in the log it could be a false positive. If you can verify they are false positives, then you have validated the detections found in the log and can then run propupd to eliminate further false positives in future scans.
There are detailed helpful tips on what to do in the README. they include :
Check the FAQ, CHANGELOG, mail archives
Check if a bug or support request has already been lodged here
https://sourceforge.net/p/rkhunter/_list/tickets
If you are sure the problem is a bug, or want it considered as a support request, then please submit it directly into the tracker system
Checking for similar reports by others using a search engine like google.
FINALLY send an email if all else fails.