I noticed one scene in ST:TNG where a fly can be seen flying near Data's head during a close-up. It somehow seemed wrong to me (it bugged me, you might say). Apparently the director didn't think it was a problem and kept it in (didn't do a re-take).
Are there bugs on Federation Starships? Has this ever been addressed? Somehow I find it hard to believe they still have pest problems in the 24th century.