It seems to me, that kirby's thumb-generation not always uses the previous generated thumbs in thumbs-folder.
I have a website which uses intensively thumb-generation (resize, crop, quality). Although all thumbs exists, kirby generates them again. But the file-timestamps of the previous generated thumbs are unchanged.
Maybe kirby does not always identify previous generated thumbs and then tries to generate them again, and on save of these newly generated thumbs it doesn't overwrite the existing ones.
Toolkit Version: 2.4.1
Kirby Version: 2.4.1
Panel Version: 2.4.1