Well other than a red card against Paul Williams (which similar incidents happened through out the whole of the KO stages), there were some shocking calls. One was just before half time, Samoa had run from their own 22 to the oppositions in the final minute of the half, their most promising period of play up till that point, and Nigel Owens gets in the way from a Mapusua pass, hits him, Samoa managed to still retain the ball, and yet he blows the wistle for half time because interfearence. That could well have been the difference in the match. He mad a lot of calls that really screwed Samoa over (not because of racism like some petty Samoan fans/Eliota Fuimaono-Sapolu claimed), but they did ruin much of Samoa's chances (and this is from a neutral perspective). One of the few things in which I think may have been harsh was Smit's yellow card (althiough it wasn't as ridiculious as some people make out, as it did seem a tad cynical). Regardless, people around the world accepted that he just had a poor game and moved on.
By the way, I'm not saying Bryce Lawrence is a great referee, more often than not he'll over compensate so he'll blow up everything a NZ franchise does, and he costed the Crusaders a game because of it. I just think it comes part-in-parcel with refereeing international matches. South Africa should have won against Australia regardless. If Lawrence was letting it be a free-for-all at the breakdown, then SA should have adapted and been equally as obstructive.