Replay systems needs to be reviewed

The biggest flaw in  the MLB's replay system happened last night.  I've always thought the challenge system, basically giving each team just one challenge per game, was lame.  What happens if there are more than one play that legitimately needs to be challenged?  Isn't the whole point of the system is to get calls correct?

Anyway, here's what happened; Angels lose challenge, while Red Sox win theirs - angels.com, "Calhoun took a couple of steps back, gave himself some momentum and fired a strong, one-hop throw to third after catching Xander Bogaerts' fly ball. The tag from Angels third baseman David Freese came just after Napoli's foot hit the base, but Scioscia believed Freese kept the tag on as Napoli's leg came off the bag. "We're going to get a little better direction from the league because Mike Napoli was out at third base," Scioscia said after the game. "The tag was on him, and in between his leg and his knee getting there, there's a gap where you can see no part of his body is on the base and the tag is on him. We lost a challenge on a play that we were pretty sure that we had, so we're going to get some direction from the league on what they saw. It's baffling. I looked at it three times here and I don't know how they missed that."

It was a great throw by Calhoun, and in my opinion, the play could have gone either way.  However two innings later, after reaching first on a single, Erick Aybar was thrown out stealing second.  But upon review of the replay, it looked like Aybar's hand had touched the bag before the tag was applied.  Yet, Angels' manager Mike Scioscia could only come out and question the call since he had already used his one challenge in the second inning.

I understand why the rulers of baseball thought having one challenge was the way to go.  They didn't want managers challenging ever close play and slowing the game way down, but as this case shows, if the purpose of the replay system is to get the call right, sometimes one challenge isn't enough.