I'm using Eclipse (Indigo) and eGit, its Git plugin. Earlier today, when I merged the contents of one branch with my master, I ran into a bunch of conflicts. While I suspect that I should have used the "Team > Merge Tool" to resolve them, as they were rudimentary in nature, I just sorted them out manually. However, eGit did not notice that the conflicts (and their in-file markers) were gone and retained the conflicted icon for each of the affected files.
Since the files involved were still not resolved according to eGit, it refused to allow me to commit them either. I found that the workaround for this was to add each of these files (via Team > Add) all over again even though they were already in the repository. I could then commit them successfully.
A little bonkers, if you ask me :S