Mohamed Salah spurned a glorious early chance but Liverpool were never close to their rampaging best from the 5-2 Champions League thumping of Roma, faced with a Stoke side battling valiantly against relegation.
The flashpoint arrived in the 87th minute when Georginio Wijnaldum drove across goal and Erik Pieters' left arm took the ball away from Alberto Moreno, who was poised to finish in the six-yard box at Anfield.
"In the second half we created enough to win the game. We should have won it comfortably," Reds captain Henderson told Sky Sports before moving on to the main source of his frustration.
"It looked like a clear penalty in play and I've just looked back on the tele and it's blatant. If he doesn't touch it with his hand it's a goal.
"It's a really poor decision from the referee and linesman, it's cost us three points."
Liverpool remain third, four points above Tottenham, having played two games more.
Last season's champions Chelsea are behind in fifth and host Liverpool next Sunday after Jurgen Klopp's men face the small matter of a Champions League semi-final second leg.
"Stoke are fighting for their lives and we've got to keep going. It's tough," Henderson added, having completed 90 minutes despite receiving lengthy treatment on a foot injury before half-time.
"We're in a good moment after midweek. We started okay but got sloppy. In the second half we had a right good go and I thought we should have won the game."
Stoke manager Paul Lambert strongly disagreed with Henderson's assessment of the referee's decision not to award a penalty to the hosts.
"Listen if that is a penalty we may as well all just have left," he told BBC Sport. "It is never a penalty.
"You can understand Jurgen's frustration about it but it's no penalty."