I've done crossfit for the last two months. without pain i hear two minor cracks from my right knee while squatting. any recommendations for me?

Depends on: If it's painful or not. We often have popping of our joints that benign ... think about your knuckles cracking. This benign popping is often felt to be related to "cavitation". If you have a pain, it's a different story. It could be related to degenerative changes, meniscal injuries or chondromalcia patella. If painful, consider getting it looked at, and avoid deep, heavy loaded knee bends.