You can check them with a free programme called MP3val. For a GUI, you may also want to download MP3val-frontend from the same website. Although MP3val can repair various kinds of structural errors, it cannot repair corrupt audio data inside a frame. Even so, patching a broken MP3’s structure might enable fpcalc to fingerprint the file well enough for matching purposes.
Alternatively, if you tell fpcalc to use a shorter length for analysis, you might be able to avoid the broken frames and generate a less precise fingerprint.
Whether you limit fpcalc or repair your files, please don’t submit AcoustIDs of broken files to the database! I know you wouldn’t do this on purpose, but I felt I must mention it.