Exiles director of rugby Brian Smith was furious after his key lineout forward was poleaxed by a Perry Freshwater elbow late in the first half.
Smith was also unhappy his side conceded a try after Delon Armitage was shown a yellow card.
Smith said: "There were two key moments in the game for us - one was when Perry Freshwater took Kieran Roche out of the game. Losing him in the lineout was crucial.
"The second was the Armitage yellow card and the resulting soft try. A seven-point gap that late in the game was always going to be tough to come back from.
"As far as Roche is concerned, he's gone to hospital. He's currently blind in his left eye. The touch judge clearly didn't have a good view, but the citing commissioner will no doubt review it.
"We had issues last week when one of our players was stamped on the head. We've written to (tournament organisers) European Rugby Cup and had no response. These sorts of things simply should not be happening on the pitch."
The Exiles director of rugby was also unhappy with his side's failure to cope with the conditions.
He said: "We didn't adapt to the weather conditions today as well as I would have liked.
"We were disappointed not to get a bonus point, but we're in a good position in the pool. We've got the Dragons at home and Treviso away and everything to play for."
Perpignan's star signing, World Cup-winning full-back Percy Montgomery, admitted he was unhappy with not playing the full match.
He said: "I was disappointed not to have finished the game.
"My knee's fine, but I got a bit of a dead leg. I'm really pleased for the team that we got the victory - it's really important for us, considering our results in the last few weeks.
"We played a smart match. We stuck to the basics and chose the right game-plan of intelligent kicking and good defence."