Hi!
Are you using the latest version of Regenerate Thumbnails? If not, it could be a problem because there’s a known error related to the “Update the content of posts to use the new sizes” option that was disabled in the latest versions. (https://github.com/Automattic/regenerate-thumbnails/issues/124)
If you think it’s unrelated, I’d like to ask you to confirm if the images are also wrong when you access them through the uploads folder. If yes, could you send us step-by-step how we could reproduce it? I tried some different approaches, and inspect the code to see where it could happen, but I didn’t find anything (the whole process work based on the attachment ID).
You could also try to disable other plugins to confirm if nothing is interfering with the filenames.
