But the Reds boss insisted his side fully deserved to take all three points away from Upton Park as they kept up their title challenge.
In a highly controversial contest, Steven Gerrard converted two penalties either side of Guy Demel's equaliser to take the Reds back to the top of the Premier League with five games of their season to play.
The first spot-kick, given for a James Tomkins handball, was the least disputed of the three goals but Demel's leveller was less clear-cut as referee Anthony Taylor appeared to overrule his assistant referee who had flagged for a foul in the build-up.
With the match hanging in the balance, it was then Liverpool's turn to enjoy the rub of the green as Jon Flanagan was brought down in the box by Adrian and the West Ham goalkeeper was penalised despite getting a touch on the ball.
"When you play against West Ham the referee will get called into more decisions because of the nature of West Ham's style - they're very physical and they ask a lot of questions," Rodgers said.
"We got a couple of decisions that I thought were penalties. The first one was clear, the second one if you analyse it we've got the reward for our enterprise and committing bodies forward.
"The young full-back (Flanagan) makes a great run, Lucas plays a wonderful pass and I think if you break it down and look at it in slow motion Jon gets a touch and goes past the keeper.
"The keeper gets a little nudge with his elbow on the ball but then as Jon's gone past him, the keeper catches his foot and he goes over."
Rodgers added: "As the manager who gets it you're pleased and if you don't get it, it's a bit contentious."
Rodgers' side have netted 90 goals in their 33 league matches this season but the Reds boss was most satisfied with his players' battling qualities at Upton Park.
"I thought we were clearly the dominant team and deserved to win," Rodgers said.
"When I first came here people were talking about the ideas and it was all football, and they probably never understood that the big part of the game is our defensive pressure, to press the ball and get it back quickly.
"At times you have to defend and we're happy to do that. It was a different type of game today."
Rodgers added: "West Ham are very, very difficult to play at Upton Park so we had to contain the physical battle and then we had the opportunities to control and dominate the ball and I thought we did that really, really well."
The game's physicality was personified by Hammers striker Andy Carroll who looked eager to make an impression after leaving Liverpool for West Ham in a permanent transfer last summer.
The England forward believes his former club will go on to lift the Premier League title this season.
He wrote on Twitter: "We were unlucky not to get something today against this season's champions."
West Ham manager Sam Allardyce was disappointed with the performance of the officials and believes his players deserved credit for their display.
"Obviously there are two decisions today - one that goes against Liverpool and one that goes against us and that ends up with controversy, frustration, aggravation and the players losing their cool," Allardyce said.
"We gave all we could give and we tried our best to upset Liverpool's winning streak and to stop them getting their ninth win on the trot.
"Unfortunately they've won the game on two penalties rather than their attractive football that they normally play.
"The players have to take a lot of credit for that but we are disappointed we didn't get anything out of the game."
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- Premier League