Leading through Jonjo Shelvey’s early strike, Isaac Hayden collided with Jamaal Lascelles and was on the floor in the six-yard area when Diogo Jota followed up his own header to score.
Within four minutes Mohamed Salah’s 22nd of the season put Jurgen Klopp’s side ahead and Trent Alexander-Arnold’s long-range 87th-minute blast sealed the points.
“We didn’t do everything right, that’s clear, but we certainly didn’t have the luck either,” said Howe, who has taken five points from his six matches in charge.
“The turning point of the game is an obvious one, I can’t understand how Mike’s not stopped the game.
“Isaac clearly holds his head immediately lying in our six-yard box with another player and that leads to the goal.
“At the time it was clear to me the game had to be stopped and it wasn’t. That is the key moment in the match.
“I couldn’t believe what I was seeing. The priority always has to be the safety of the player, we talk a lot at the moment about head injuries and I felt that was a wrong decision and we were harshly treated today.
“He was treated and taken off to the side of the pitch and still didn’t look 100 per cent himself.
“It follows a similar pattern where the rub of the green has gone against us. You play at Anfield and have the lead and then suddenly they get the goal and the crowd are up.”
Liverpool manager Klopp, who saw his side become the first in English history to record 2,000 top-flight victories, understood Howe’s frustrations but did not see it clearly enough to comment.
“I saw a player down when we scored a goal there was only one player down. I spoke to the linesman and he said ‘all fine’,” he said.
“I cannot judge the situation down there. We were not involved in the incident as far as I know, they jumped into each other if things people told me are right. I can imagine Eddie is not happy about that.”
Klopp’s side achieved a relatively comfortable victory without Virgil Van Dijk and Fabinho, who along with Curtis Jones, tested positive for Covid on the morning of the game to throw their plans into disarray.
The Reds boss remains hopeful the situation has been contained but expects there to be more positives in the coming days.
“The situation is difficult for us, the whole world, and we pretty much woke up this morning and had three positive cases,” he added.
“The process we follow is a lateral flow test and then go back into the car and in this moment we had three positive tests, which is not too cool.
“We had to make the decision to send the boys home: three players out, two of them would have started today but it was not a reason to cancel a game tonight or even ask for it.
“We will see how it develops. This virus is around us so long it is unlikely it will stay at three.”