Diogo Jota's 10th goal of the season came while Isiah Hayden lay on the floor with a head injury.
Eddie Howe said that it was unjust that the Reds scored while the man with the head injury lay on the ground.
Jonjo Shelvey gave Howe's side a lead but Diogo Jota's goal was awarded by the referee despite the fact that he was in the penalty box.
He said that one of the players was holding his head while on the floor.
The game should have been stopped because the focus should have been on his welfare.
"We had two players out of the game that would be defending that cross and I think that's very unjust," Howe said.
Trent Alexander-Arnold put the game beyond doubt with a fine strike three minutes from the end, after Mohamed Salah had scored his 22nd goal of the season.
Howe said the first goal was the turning point.
He said he couldn't understand how Mike hadn't stopped the game. "Isaac was lying in our six-yard box with another player and of course that leads to the goal."
The game wasn't stopped for me, that's a key moment in the match.
The player's safety is the priority. I felt that it was a wrong decision to talk about head injuries.
There was no acting from the player. He was not up. We paid the price for him not continuing.
We've been harshly treated today and it follows a similar pattern of other games where we've not had the rub of the green or the decisions going against us.
The crowd were in the game after Jota's goal and that made it very difficult for them to stay in the game.
Howe said that the injury to Lewis looked bad.
The former Bournemouth boss said: "It's not the time of year for us to lose players and fingers crossed he's the only player who will probably go into the Christmas period now in any doubt."
Allan Saint-Maximin was replaced by Callum Wilson, who was rested.
Howe didn't know what the French player's injury was before the game.
Howe said they don't want to lose him for a long time.
I was surprised he didn't blow the whistle.
The referee blows his whistle when a player goes down holding his head. You can see players holding their heads, you can also see that they are waving it. He doesn't blow his whistle.
If there is a suspicion of a head injury, you would expect to see it stopped. We expected it to be stopped, but players are going to have to start defending their six-yard box first because referees are not stopping the game.
