"We knew it was always going to take a dodgy decision to break the deadlock and unfortunately it went against us," said Monk.
"It's gutting really because it changed the course of the game."
The win for second-place West Brom puts them 12 points clear of the Swans, leaving them an uphill task to reach automatic promotion, although they remain in the play-offs.
It was the Welsh side who had dominated large periods of the game, but neither side really looked like scoring before Barnes went down in the box with minimal contact from Angel Rangel.
Ishmael Miller wrapped up the win in the final minute catching out Swansea who were pressing for a leveller.
"It's not becoming a surprise now," Monk added.
"I hate moaning about it but it seems to be game after game now that big decisions are going against us.
"I was right behind Angel at the time and knew he [Barnes] had dived so I was thinking the ref was blowing to give us a free kick or something like that, and when he pointed to the spot, I couldn't believe it.
"We've just watched it back on the laptop and if anything it's a yellow card for the lad for diving, so it's hard to take."
Just 10 days ago, the Swans were denied a clear-cut penalty at fellow promotion rivals Nottingham Forest when Darren Pratley was brought down by Chris Cohen, before they were eventually beaten 1-0.
And manager Paulo Sousa has hinted that he may take his grievances as high as Uefa in a bid to improve refereeing in the game.
"The club has asked if I'm interested to expose all of the decisions during the season that have been mistakes that cost us points not only to the FA, but to Uefa and you guys," said Sousa.
"We want to help the referees make better decisions, but we will see in the future."
Source: BBC Sport
Source: BBC Sport