I guess anything is possible if you misconfigure the tools you use badly enough, but I am still dubious that 1000 images have gotten embedded in multiple files. You can set MB to search for "missing artwork" and automatically embed it, but that would not embed 1000 images it would take files with 0 images and give them 1 image and then not affect them again.
I think you should pull up one of these files in the tag editor (shift+enter) and then go to the artwork tab and hover over each of the the pictures (or as many as you can in a sitting) and see how they're really stored. Any time anyone here has come with this problem, it's been an issue of rogue image files sitting in folders.
Or open the directory where the files are in mp3tag and display the artwork column and see how many are actually embedded.
I don't think there's a way to delete them all at once in MB (I may be wrong - I've never mistakenly embedded 1000 images in a music file before so I'm kind of flying blind) but I know if you go the mp3tag route you can right click the displayed image and select remove cover and then save. That will wipe it so you can start over. If you select all the problem files and do this on the box where the image would be, it will clear them all out.