It sounds like your stash included an untracked file that was subsequently added to the repo. When you try and check it out, git rightly refuses because it would be overwriting an existing file.
To fix, you could do something like deleting that file (it’s okay, it’s still in the repo), applying your stash, and then replacing the stashed version of the file with the in-repo version as appropriate.
Edit: It’s also possible that the file has only been created in the working tree without having been added to the repo. In this case, don’t simply delete the local file, rather:
- move it somewhere else
- apply the stash
- manually merge the two file versions (working tree vs. moved).