The Brazil attacker, captaining PSG with Marquinhos and Presnel Kimpembe absent, was fouled twice in the space of three minutes.
He was visibly upset after the second foul, by Steeve Yago, exchanging words with the Caen player.
As the game resumed, Neymar continued to complain before walking down the tunnel to the dressing room in the 57th minute.
The world's most expensive player was replaced three minutes later by Kylian Mbappe.
"He has pain in his thigh, we will see tomorrow (Thursday) if it's an injury or not," said Pochettino. "We will see tomorrow after the scans.
"I don't want to talk about the opponents' way of playing. But during the match, there is a feeling of having little protection. But it's not only in this match."
Neymar, although appearing to be moving quite comfortable, was grimacing while holding his thigh.
Nevertheless, PSG will be worried, with their Champions League last-16 first leg against Barcelona at the Camp Nou on Tuesday.
But Pochettino defended his decision to name a strong starting XI which included Neymar despite the forward only featuring as a substitute against Marseille on Monday (AEDT) due to a stomach problem.
"Every game is important. I believe that PSG must win every game," said the Argentinian, who took over from the sacked Thomas Tuchel last month.
"If we had lost, you would have criticised me for not having given importance to the French Cup. We make the decisions, we analyse, we try to find the best team."
The holder did enough to win despite finishing the game without their stand-in skipper, as Moise Kean's 49th-minute goal, assisted by Neymar, proved to be the winner.
PSG was never in serious trouble as they moved into the last 32.