The 34-year-old dished out three yellow cards during the match - two to one player as Blues wing Matt Duffie was given his marching orders in the 67th minute.
Duffie’s first infringement was for offsides in the first half after a string of Blues penalties early on, and his second came when he was adjudged to have dived illegally on Stormers wing Cheslin Kolbe, who had been tackled.
It was a contentious issue in the game, with many on social media suggesting that the Blues wing had been given a raw deal, but it wasn’t the only time that Van Heerden was put under the spotlight.
Few could argue with his decision to yellow card Eben Etzebeth on 20 minutes, but when Shaun Treeby got away with a high tackle on Blues flyhalf Piers Francis on 47 minutes, the visitors would have been seething.
After consulting with TMO Shaun Veldsman, Van Heerden decided that a yellow card was not required and Treeby received a stern talking to instead.
Francis, meanwhile, was knocked out cold and had to be taken off the field not to return.
Speaking after the game, Blues coach Tana Umaga said he could not comment on the standard of officiating and that he would have to follow the right “processes” to voice his concerns, but he still managed to make his views quite clear.
“Obviously when you have people taken from the field and things like that it makes it difficult when you’re one man down,” he said.
“I’m not allowed to answer questions about refereeing decisions and the way that goes. We’ve got a process that we go through and we’ll do that, definitely. We’ll make sure that we do go through that process and that something is done from it.
“There were some key calls, obviously, and you saw how difficult it was to play with 14 men especially at the back end of a game.”
The former All Black centre then had another little stab, saying that New Zealand teams often found themselves on the end of some harsh refereeing when touring South Africa.
“We understood that coming over here. We talked about it,” he said.
“There has been a lot of yellow and red cards over here in South Africa every time New Zealand teams play. It wasn’t as if we didn’t expect it, but it’s just the way it goes.”
Skipper James Parsons also weighed in, saying that it could have been a different story had the Blues “adjusted to the ref a bit better”.
For Fleck, though, that will not matter. He has broken a four-match losing streak and the Stormers have now beaten New Zealand opposition twice this season.
“Their intensity on defence … they had a very good plan in place to put pressure on our runners and slow our ball down,” Umaga conceded.
“They were just relentless in what they were doing. It was a difficult day.”