Could it be this this situation:
Say that in an album, half the tracks have cover art, half do not. The tracks with art all share the same image, auto-named by MC per the album-artist.
Then a DIFFERENT image is applied to one or more of the no-art tracks. MC auto-names it, also per the album-artist, so MC gives the new image the SAME NAME as the existing image -- overwriting it.
Since the cover art image path/name is the same before and after, the tracks that showed the old image now show the new image -- even though these tracks were not explicitly touched by the user.
It doesn't matter whether the new cover art is acquired automatically or pasted-in manually. The new-image-replaces-old-image behavior is due to the images being path\file-named identically by MC per the cover art naming formula.
Of course, what MC is doing is reasonable -- exactly what it should do, per the notion that an Album is what has cover art, and per the cover art naming formula. But it can be a big surprise because altering one track can alter others. My situation is both better and worse because I store ALL my cover art files in ONE folder. This has some benefits in my situation, but increases the chance that MC will overwrite one image file with another of the same name.
What makes this image change undesirable is when the "cover" art isn't really the cover, it is some other image like the artist's photo or whatever, and the user WANTS different tracks of the "album" to have different images. I encounter this a lot with songs that appear in several albums, different compilations, etc.
My workaround, before adding/changing the image of SOME of the tracks of an Album, is to temporarily rename the Album (by adding "x-" to the front or similar) of the tracks about to receive the new image. Thus the new image file is given a slightly different name by MC. After it is saved and assigned to the tracks, I rename the Album correctly, but this doesn't affect any tracks because the image file path/name has already been assigned to each track. Of course, if in the future I want to replace the image of just ONE of the tracks, I risk having ALL the tracks with the same Album name get the new image, so I do the same trick again, temporarily renaming the Album of the tracks I want to retain, or change, but not both. The temp Album renaming doesn't give me any odd folders because I don't store songs or cover images in folders named after albums. (Not of much value in my library; I name my folders per genre and within those in folders of first letter of artist's last name.)
Other threads have discussed possible MC changes such as a track-level checkbox that tells MC to not mess with the cover art image path/filename field, coupled with the ability to manually edit this field (and/or via search/replace).