Trundle did not touch the ball and it rolled into the net, with referee Ray Oliver insisting that as Trundle did not touch the ball he was not offside following the latest rule change this summer - and that the goal had to stand.
It proved to be a decisive goal, handing the Swans a 3-2 victory.
But Hendry raged: "He's made a basic error, but he won't admit he's made a mistake.
"I went into his room, but I had to walk out because I was about to lose my cool.
"He said Trundle wasn't interfering, but yet he's standing in front of people in front of the goal. It's incredible, but it's cost us a point.
"I have to take responsibility if we get beat, but he says he hasn't made a mistake. Lee did very well and has done everything I would expect my centre forward to do, but he was active and the referee should admit that."
Swansea manager Kenny Jackett, whose side stay top of the table after the win, said: "My first thoughts were that Lee Trundle touched the ball for our third goal but having seen it again he clearly hasn't.
"He has reacted very intelligently because he must have known the flag was up and that's great awareness.
"It's a grey area and I can imagine Colin Hendry is not happy but they are the rules and teams score goals from it."