Lyon were incensed after being denied a second-half penalty as they slipped to a third straight loss in Ligue 1, with Rennes claiming a 2-0 win on Sunday.
Rennes took the lead in only the fifth minute, as a terrible header from Lyon centre-back Marcelo sent Wahbi Khazri running clean through on goal, and the former Sunderland winger made no mistake to slot in his seventh league goal of the season.
But several Lyon players were furious in the 57th minute as referee Amaury Delerue waved away appeals for a spot-kick after Nabil Fekir was tripped by Jeremy Gelin just as he prepared to shoot on the edge of the six-yard box.
Fekir argued for over a minute with the officials, before he and team-mate Bertrand Traore were both booked.
"I'm not sure tonight's referee was in the best position to officiate this game," Lyon president Jean-Michel Aulas told Canal+.
"There were a number of incidents in the away game at Caen (in December, which Delerue refereed), which were reported by the press.
"We won't replay the match and it won't change the way we referee each other, and they are pretty good referees. Sometimes they make mistakes and sometimes they don't see obvious things."
The attacking midfielder came close to a late equaliser, but saw his left-footed strike fly narrowly wide.
Midfielder James Edward Le Siliki grabbed a second for Rennes in injury-time as Lyon lost crucial ground in the race for Europe.
Marseille are third, just one point behind Monaco, who moved up to second by thrashing Angers 4-0 on Saturday, after OM's draw at Saint-Etienne.
Paris Saint-Germain stretched their lead to 12 points at the top as a Neymar goal gave them a 1-0 win at Toulouse ahead of their midweek Champions League clash with Real Madrid.
Earlier on Sunday, Nantes retook fifth spot as Emiliano Sala scored twice in a 2-2 draw with Lille, while Strasbourg edged out Troyes.