Have a look at your goodinfo.cfg, which contains info about the different flags and the corresponding subdirs. If you have a ";n" at the end of a line, the goodtool won't list files containing that flag in the missing.txt file.
TikTok is right, by default bad dumps are excluded - they won't show up in the missing list, even if you don't have them.
If you don't want files to be excluded from your missing list, just delete the ";n" entry, or - a more radical solution - delete the goodinfo.cfg file

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