When exporting "Current Frame" you get a .jpg file (for JPEG). Some apps write it as .jpeg and some put them in upper case. These are all viewed as different files by macOS. So even if the name portion of the file is the same, if the suffix is different, to macOS, they're different files. I've tested this extensively, because I swore Pixelmator Pro was doing this same thing at one time. Then I saw the suffixes were different, and that solved that. Maybe this isn't your issue.
I remember Mojave, and yes, it always had a but when you click Show File, that it wouldn't. Used to drive me nuts.
But Luis is correct, file naming and duplicate file names are handled by macOS, not Motion. Motion is simply making system calls to do the work for it. So the issues is in Mojave, not Motion.