2006 Nissan Altima Occasional Knocking

A couple of weeks ago, I started noticed a slight "knock" every so often while driving. At first, I thought it might be the brakes (since I just had them and my rotors replaced), but the knocks were so few and far between that I didn't worry too much about it. Today, however, I noticed the knocking a few more times just on my drive home. It seemed to happen when accelerating, almost when the car was switching into 2nd and 3rd gears. I checked the transmission fluid while the car was running, and it appeared to be okay, though it was slightly under the "HOT" reading. Any thoughts?
Thank you!