Make sure that your seat isn't too high or low as that could be putting strain on your knees.
Also make sure that you aren't riding in too high of a gear as that can aggravate your knees too.
Trust me when i say, knee injury SUCKS!
Yeah I actually tried putting my seat up a little the other week and it made it a bit better, so maybe I just have to put it up even further! Thanks Sal!