What probably happened is that you fled to the commons area, then reentered the dungeon. Some dungeons/instances won't reset if you re-enter them within the time limit. Some, like Ironworks, and the Plague Oni instance, will actually bug, and you won't be able to continue it.
You can fix it by entering the dungeon/instance and then exiting it back through the door you entered it (don't teleport out, as that won't fix it). You'll get a warning about leaving the dungeon. Ignore it and leave anyway. Then you can re-enter, and the instance will be reset from scratch.
