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Paul Warne felt Swansea's controversial third goal should have been ruled out for handball as his Rotherham side were beaten 4-3 at the Liberty Stadium.
The Millers suffered a crucial defeat as they battle to avoid dropping out of the Sky Bet Championship, with George Byers scoring Swansea's third goal.
Byers' strike appeared to take a slight touch off Kyle Naughton on the way into the net and Rotherham's players screamed for handball against the Swansea defender.
Referee Keith Stroud awarded the goal and Rotherham never recovered.
"You'll not be surprised to know I think it was handball," said Warne. "Throughout the season we've had some bad luck as all clubs have, but I've never seen my players react the way they did.
"The fact it was the only goal of seven not to be played on the big screens speaks volumes. When I watch it back on the bus on the way home I could be wrong, but I'll be amazed if I am. I think it hit his (Naughton's) arm and was deflected away from our goalkeeper."
Wigan's shock win at Leeds means Rotherham remain in the bottom three above only Ipswich and Bolton, who have already been relegated to League One.
"It's hugely disappointing being the manager of the team that lost, but I'm not disappointed in the performance. It's unfortunate we've come away with nothing," Warne added.
"We've got three games left. I don't know if we'll survive, but we have to win all three."
Rotherham led 2-1 at the break thanks to Michael Ihiekwe's slight header and a clever strike on the turn from Matt Crooks. Swansea striker Oli McBurnie scored in between the two Rotherham strikes as he headed home Matt Grimes' corner for his 20th goal of the season.
Byers was a half-time Swansea substitute and was soon at the centre of the action after Barrie McKay had made it 2-2 with a rare header form a pinpoint Daniel James cross.
The shot from Byers was already goalbound, but Rotherham were convinced it went in off Naughton's hand as captain Will Vaulks led their appeals.
McBurnie looked like he had made the game safe when he found the bottom corner, but Vaulks netted Rotherham's third and they pushed hard for an equaliser in eight minutes of stoppage time.
Swansea goalkeeper Kristoffer Nordfeldt saved brilliantly from Michael Smith late on.
"It's not easy to play against Rotherham. They're big and use their strengths well. Even though the opposition are fighting for their lives, we came through," said Swansea manager Graham Potter.
"They made it really difficult for us, but credit to the boys. They've scored four goals and Kris had to save us as well. We attacked quite well and overall I'm really pleased."
On Byers' goal, Potter said: "I couldn't see from where I was. I've not seen it back, so I don't know."
