My site (3.4.0) has 2 separate channels with this issue, the only channels with multiple File fields right now. When creating a new entry in either channel, the last file I upload in any File field replaces all other File fields.
So after I've added the image file in the image field in the 1st channel, I upload an audio file from a different file upload folder in an "audio" File field. When I do this, it replaces the file for the image field also with the audio file, so both fields now have the audio file (regardless if the image field could accept the filetype). If I do it in reverse order, both fields will have the image file.
Another channel has a Grid field, in which one can choose multiple different files and file types for up to 8 grid entries. The same thing occurs: after I've uploaded/chosen 1 file, the second file I upload replaces both so I have duplicates. This continues such that the last file I choose will replace all the others for up to 8 duplicates. Editing / replacing any file while still creating a New Entry will have the same result, all files will be changed at once.
The only work-around I have at the moment is, after saving the New Entry, if I edit that entry I can change any file without it changing all the others. But this isn't user-friendly, I don't want to tell all users they have to save their entry and then edit it to make multiple files work. Please help if you know what's going on.