First, check git status.
As the OP mentions,
The actual issue was an unresolved merge conflict from the merge, NOT that the stash would cause a merge conflict.
That is where git status would mention that file as being “both modified“
Resolution: Commit the conflicted file.
Solution: in this case, simply add and commit your local file.
You can find a similar situation 4 days ago at the time of writing this answer (March 13th, 2012) with this post: “‘Pull is not possible because you have unmerged files’“:
julita@yulys:~/GNOME/baobab/help/C$ git stash pop help/C/scan-remote.page: needs merge unable to refresh index
What you did was to fix the merge conflict (editing the right file, and committing it):
See “How do I fix merge conflicts in Git?“
What the blog post’s author did was:
julita@yulys:~/GNOME/baobab/help/C$ git reset --hard origin/mallard-documentation HEAD is now at ff2e1e2 Add more steps for optional information for scanning.
I.e aborting the current merge completely, allowing the git stash pop to be applied.
See “Aborting a merge in Git“.
Those are your two options.