I guess you're talking about someone trying to jump up and bat the ball away before it crosses the crossbar. There's no NCAA rule against that (see 9-4-1b).
The interesting thing in this scenario is that if the Team B player who is positioned in the endzone jumps up and blocks the kick, he must then recover it. If it remains in the endzone and Team A recovers it then its a touchdown for Team A. This may be the reason team's don't position a player in the endzone to try and block a field goal attempt. That, plus the fact that the crossbar is 10 feet off the ground (height of a basketball goal) and there are very few players who can jump high enough to block a ball that's higher than that, much less while they are wearing football pads!
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