Blues prop Ofa Tuungafasi was awarded a try in the second half, with the Chiefs' cries for a knock on in the grounding going unheard, while Chiefs flanker Pita Gus Sowakula had a late try awarded, then overturned by the TMO.
"We didn't get the rub of the green," Cooper said after the game.
"Tries went their way which maybe should have been looked at and weren't looked at. We were awarded a try and unless the TMO got another view, I couldn't understand why Pita Gus's wasn't a try."
Back in South Africa, the Crusaders were forced to settle for a draw against the Stormers after TMO Marius Jonker called back play when it appeared Sevu Reece had scored a spectacular match-winning try.
Jonker alerted referee Nic Berry to what he described as a "clear and obvious" forward pass by Braydon Ennor, although replays were inconclusive on whether it came out of Ennor's hands backwards and was carried forward by simple momentum.
Crusaders assistant coach Brad Mooar suggested the pass being made with a line in sight probably didn't help his team's case.
"We were obviously disappointed, we liked the first decision better, but at the same time that's what the officials are there to do. I suspect the pass, having been on or around the halfway line, the presence of the line probably didn't help, but how do you sum those up?
"That's not the reason we drew the game. We had our opportunities and that was one of them. It was still great play, just ruled forward."