I run in the evenings, and I'm a little slower if I've been cycling all over town during the day. If I can't run as hard as I want, then I just go longer. Both my lady and myself commute by bike 5 days a week, run as many errands as we can via bike, and run 5-6 days a week. The only noticeable side effect for me is that it doesn't take long to burn off the winter fat. The Lady G'Cakes will get an overuse injury at least once per summer, but it's usually in the ankle and I usually blame soccer, not biking.

You could've stressed your knee biking, then aggravated it into injury when you ran. I'd make sure that the fit on your bike is correct, an ill fit bike can mess up your knees.