Switch back to platform pedals and see if the problem clears up. Lachlan Morton did that in July during his solo alternate-Tour de France, riding more distance than the official race and finishing sooner. Morton is an experience pro cyclist, part of the EF team, but is better known for ultra-distance cycling. He developed some ergonomic problems during the first week with clipless and switched to platform pedals for most of the rest of the tour, including some distance wearing flip-flops or sandals. Morton said there was no significant difference in his power and speed between clipless and free-footing it with platform pedals.
Meanwhile, sure, muscle strain can cause some minor problems with patella tracking, which can cause some annoying clicking. There are simple support braces that can help with patella tracking. Meanwhile, try some home physical therapy (there are zillions of tutorials on YouTube, but only a few good ones), and switch to platform pedals while giving the knees a chance to recover.
With no foot retention it's easier to move the feet around on the pedals to suit yourself. With foot retention - clipless or toe clips -- you're locked into a narrower range. If the setup isn't right for you the only way to fix it is to move the cleats -- but most cleats offer a very limited range of motion, even with plenty of float.
If you do switch back to clipless, go easy for the first couple of weeks and pay careful attention to getting an ergonomically friendly bike setup.