Is there a way to make Git mark a file as conflicted?

If the index is already in a conflict state, simply check out the file with the --conflict=merge flag:

git checkout --conflict=merge file

If the index is clean because the unresolved file has been [erroneously] added, just reset it before checking it out:

git reset filegit checkout --conflict=merge file

This will allow you to resume conflict resolution normally (e.g., git mergetool).

NOTE: Promoting a comment to @jakub-narębski's answer into its own answer by request from @fourpastmidnight. :)

You can get contents of file with conflict markers using git checkout --conflict=merge -- file, but if you have cleaned up index by using git add file (or if GUI did that for you) it wouldn't work.

There is git update-index --unresolve, but it is hacky, and does not work very reliably. I think the state it restores would be not enough for git-mergetool.

You would probably have to redo merge, or use git update-index --cacheinfo to manually set stages version... git-stash can help you preserve correctly resolved conflicts.

The most elegant solution would be to prevent this problem from the very beginning:
git config --global mergetool.[tool].cmd [command-line call]
git config --global mergetool.[tool].trustExitCode false