You could do an analysis of the output from perl -MO=Xref yourfile.pl. If there is a subroutine listed in the "Subroutine (main), Package main" section that's not listed in the "Subroutine definitions, Package main" section, that's a possible problem to look into. The same goes for other packages too. I'm just theorizing here, as I'm not fully up to speed on B::Xref, but it does look like a good place to start if you simply wish to check to see if subroutines being used match subroutines actually defined.

This doesn't get you very far with object method calls though. ...I guess that's what comprehensive test suites are for. ;)