That's precisely what it's supposed to do. If you update the Tripwire db every time you "initiate an action that causes monitored files to change" - then it does a _magnificent_ job of telling you when someone _else_ changes those files.

You need to run 'tripwire --update' every time you run 'apt-get update' or 'pip install foo' or 'npm install bah' or whatever - then you wont get that storm of false positives.