TOOLS-4016 showed a case where a (longtime) MongoDB employee missed the first warning on this limitations page.
The problem is definitely not the user in this case; the tool is at fault for not warning about the conflict.
mongodump should create files with O_CREAT | O_EXCL. This will yield EEXIST errors when those files already exist. Thus we can easily give a warning like:
File `test.COLL` already exists. Blah-de-blah
We can be more aggressive here about correctness if we want. For example, we could require archive format in this case. Or just leave it as a warning, optionally detecting which namespaces are in conflict.