The Shirimpers boss said his side had been beaten by a “freak moment” after Antoni Sarcevic’s blocked shot looped up and clipped the crossbar, leaving keeper Mark Oxley stranded as Shaun Miller scooped the ball into the net eight minutes from full time.
There were claims from the Southend camp that the ball may have drifted out of play before hitting the woodwork and being spilled by Oxley.
“I last saw a goal like that 12 or 14 years ago, it’s held up in the wind and hit the back of the crossbar before somehow spinning back round,” said Molesley after the final whistle.
“There’s a shout for it being off the pitch but it’s a real freak moment.
“In the second half I thought we looked really solid and we didn’t look like conceding at all.
“It’s taken a freak moment to undo us and their boy has done well to turn it home.
“But he must have thought all his Christmases had come at once there."
Southend remain 22nd in the table, while Bolton climb up to 10th.
Ian Evatt had some words of consolation for his opposite number, insisting the Essex men were better than their league standing suggests.
But that couldn’t cheer up Molesley after what had been a tight second half.
"You have to be alive and alert until the whistle is blown and we weren’t," he said.
"It was probably the only time we weren’t switched on and we’ve been cruelly and harshly punished.
"It’s a cruel game and it's agonising to have lost."
Evatt added on Miller's winner: “It was a bizarre goal but they happen.
"We saw our goalkeeper make an error on Wednesday night (at Mansfield) and you just have to be there to put them away, fortunately for us, Shaun was there.”