spinning

I set up my bike on the trainer and I spun for about 45 min. The front of my left knee kind of aches, I would not call it painful but it does not feel right or good. It felt weird while spinning and even now after I stopped. The muscle that is healing felt totally fine. I'm not really sure what is off or maybe I'm just being ultra sensitive/cautious right now. But to be honest I'm getting scared of riding.. Which is horrible because it is my strongest part of triathlons...