File writing/reading error detection (repeated sections)

Unless there are tiny digital dropouts or sharp waveform discontinuity at the in and out points where the card skipped.

This is a high chance (and only one, I would say).

Wavelab Global Analysis Errors/Glitches will find those. I usually set for high threshold and sensitivity (like 99 and 99), but you could try lower as well, although if you do you might get a lot of false positives.

The Error Detection tool (specific Tool window) is certainly a better alternative.
Another visual tool is to use the Spectrogram: you can generally see when when there is an unexpected click.