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I wonder if that frame had a slight glitch when writing or is on a weak part of a HDD. Formats like TIF, BMP and JPG are surprisingly robust when it comes to read/write errors. could just be that frame didn't completely write all its metadata fully in the header information. You could try running the subs through a batch process to resave then to same or different uncompressed format and try those to see if they register/stack properly. That would point towards a read/write issue rather than a registration issue.
If it happens again using the same subs but resaved (this should give you cleanly written files on different hard drive sectors so failing hard drive wont fail the same way with the new files and if it does fail stacking you can look at your registration settings, maybe your camera is starting to get more noisy with age or climate ? its just considering the factors and testing/eliminating to pin down exactly why. obvious suggestion i overlooked, does your software log what it does? you might find information that indicates what caused that file to not register.
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