Yep, some anti-virus / anti-malware / anti-spyware programs can report back "false positives".
Also be careful that the anti-whatever program you're using is a reputable one as some of them can cause more problems than they fix, or some are even themselves a virus or spyware.
And/or, also be sure to go into the Settings of the anti-virus program and adjust some options accordingly. For example, you might want to have the anti-virus program prompt and ask you what to do if it finds what it thinks is a threat/virus, or to "quarantine" it, rather than automatically delete said files, as in the case of a "false-positive", it could then automatically delete a good file if you had the setting to do that. Or you could also set-up a white-list of folders/files that you trust.
After using Avast for the last couple of years (Before that I was using Anti-Vir, which was good for a while, but again seemed to get worse in performance and service over time), with some recent updates to it's engine, it seems it was becoming more and more "bloatware" (it seemed to be bogging down my computer sometimes, and only seemed to get worse with each new engine update), and I've also had a few "false positive" reports from it when I knew that the programs it was reporting as "suspicious activity / potential virus threat", were programs I trusted and wanted to run (Such as the Steam-client and some games in my Steam-Library).
I've just recently switched over to Microsoft's Security Essentials:
http://www.microsoft.com/security_essentials/So far in my experience with it, it seems like a good free anti-virus / anti-spyware / anti-malware program that does the job well and so far no false-positives. Plus, it doesn't seem to slow my computer down, and so far hasn't conflicted with other programs or caused slowdowns (such as when playing RailWorks or some other games). So it looks like Microsoft's got their Security Essentials program done right. So if you're looking for a good, and free, anti-virus I think I'd recommend it.