I also couldn't keep track of the ninja who weren't on Kakashi's team until after the Forest of Death bit. I definitely didn't have a good sense of which genin was on what team until my second time through though. (Watching the anime helped there.)

I've noticed that I tend to read fight scenes too fast, especially in scanlation, which means I'm often like, "What just happened? How did he do that? Eh? Help?"