We've all probably had a skill that sticks right during a run. It always seems to be my "Q" key when it happens to me, SC or heals. I finally figured out how to fix it instead of starting a UG run over. Wouldn't you kmow, a mere 3 days before the bug fix gets implemented.
If this happens to you, try swapping pulse into that skill slot and once it's ready, shoot a pulse off. If pulse works, swap your skill back in and try that skill. It's always my Q key because pulse is the other skill key. (key mapped to something diff than default)
Obviously, you'll need to get past whatever fight you are in before you can do this, but give it a shot.