Currently, if a repository has a dirty submodule, SourceTree goes through this workflow:

1. Open the commit dialog for the superproject
2. Stage your superproject changes and click Commit
3. The submodule check window appears.
4. Click "Open" on the submodule and commit the change
5. Return to the superproject and click "Refresh".
6. The superproject commit continues automatically WITHOUT staging the new submodule commit

I think the submodule check screen should not continue automatically; it should return to the superproject's commit dialog and allow the user to stage their change to the submodule. This will help prevent forgetting to commit the submodule's new checkout. If the user really wants to ignore the dirty submodule, they should click "Skip".