Save track As… allows me to overwrite a file without a pop-up asking if that is ok. According to the test module, saving a file under an existing file name (replacing a file) should result in a confirmation pop-up.
If I choose to save a file as “myfile.bed” and I select the “.bed” extension, the system checks to see if there a file called “myfile.bed” and then it saves a file called “myFile.bed.bed”. If I save it the same way multiple times (“myfile.bed” and I select the “.bed” extension) then it never prompts me to confirm that I want to replace the file. It overwrites the file myFile.bed.bed file.
If I then save a file with the name "myfile.bed.bed" and I select the ".bed" extension, it asks if I want to replace the file. If I say yes, it write a new file called myFile.bed.bed.bed (leaving the myFile.bed.bed in place).
This seems very closely related to issue IGBF-1128.

The system should check if the file already exists and prompt the user to confirm that an existing file should be replaced. It does this. But it adds the file extension AFTER it does this check. It should add the file extension first, then check if that file name already exists.

We should also add a check to see if the given name already ends in the desired file extension.

To see the Save Track As... option, right click on a track label.
This is true for both annotation tracks and graph tracks.

I think this is a beginner issue, but I say that without having looked at the code, it might be more complicated.