Identifying Bad Sectors on magnetic stripe, or noise in signal
Typically you wouldn't directly use time-domain samples of a signal to declare its integrity (or lack thereof). I'm not familiar with the magnetic-stripe specification, but in most systems, any encoded data is protected by some form of checksum. This checksum is usually located in the same stream of symbols as the data of interest. Many systems also include error-correction coding, to provide tolerance to some number of symbol errors while still being able to recover the encoded information successfully.

Once the signal has been demodulated and you have recovered the symbol stream, you would calculate the checksum of the recovered data and compare it to the checksum that you read from the medium itself. If they match, then you can assume that the data is correct. If they do not, then you can try re-reading the medium again, or after some number of tries, you might declare it as a bad or damaged region.

This all begs the question, though: what is your goal of marking these regions as damaged? What will you subsequently do with the damaged areas?