If I try to import https://et.wikipedia.org/wiki/Fail:Image002.gif then it gives an error as one of its older versions is identical to https://commons.wikimedia.org/wiki/File:Maks.gif which was imported to Commons earlier. It occassionally happens that new version is accidentally uploaded under wrong title or file is intentionally overwritten, but it then then gets reverted and new version is uploaded under new title. I believe it should be then still possible to import files under both titles along with their entire file histories.
I recently wrote about other kinds of checks on old versions (T216516#5349251) which seem unwanted to me. Maybe there is some generic solution to this.