Clement Grenier missed a penalty for the hosts before Odair Fortes struck in the 77th minute to give the northern French side a shock 1-0 win.
In a game disrupted by torrential rain - with officials forced to suspend play by 35 minutes at the start of the second half after a downpour - Remi stressed that his side showed sufficient quality to at very least avoid defeat.
"We are very disappointed after the game we've played," the 47-year-old Frenchman told journalists after the game.
"We did not play well in the first half, this is obvious, but we did everything we needed to do in the second half in order to win the game.
"I think as a minimum, a draw would have reflected the game more fairly."
The game represented Lyon's second loss in five days, after they slipped to a 2-0 defeat against Real Sociedad in the first leg of their Champions League playoff on Tuesday.
Though Grenier was willing to accept a great deal of the blame after the game, he dismissed talk of an early-season crisis at Stade de Gerland.
"My penalty miss was the turning point of the match," the 22-year-old Frenchman said.
"But despite losing at home, it is only at the beginning season and we have a return match Wednesday in the Champions League. We cannot talk about a nightmare start to the season right now and we will recover."