They had taken a lead five minutes into the second half through Jordan Brown but Charlton levelled two minutes into stoppage time through Macauley Gillesphey before Kayne Ramsay won it five minutes later.
It meant the Addicks replaced the O’s inside the League One play-off zone, simply adding to the mood of the boss.
We have to pick ourselves up because it’s three defeats on the spin,” said Wellens.
“We didn’t start well. We were poor, went too long and more or less all game, their chances came from us.
“The two goals they got came from them being on the edge of our box and our game management was really poor.
“The second goal was a blatant foul on our goalkeeper after Matt Godden barged into him but you’re dealing with people that aren’t capable of refereeing League One games.
We should have scored a second because we had chances. The difficulty came when they took all the small players off and brought on giants and they kept shelling it forward.
“It was a good tactical substitution from them but we don’t have any fit centre-backs. If we had, we could deal with that.
“We’ve been giving the ball away in silly areas. We’ve been here before and we need to iron out these mistakes and look forward to the next few games.”
Brown’s goal was a superb strike from 20 yards and Orient had a golden opportunity to extend that advantage just two minutes later.
Striker Charlie Kelman got in but was denied by keeper Will Mannion and the miss was to prove costly for the home side as both Charlton goals came from corners sent in by substitute Alex Gilbert.
It led to an outpouring of emotion from Charlton boss Nathan Jones, one he acknowledged may have been on the cusp of too much.
He said: “I got abused constantly by the Orient supporters throughout the 90 minutes and as managers you have to put up with that.
“There was emotion and that’s why we do the job. Orient are a good football team and if I offended anyone then I apologise.
“I thought we started both halves poorly and it took a great strike from them to get past us but after that I thought we were good value for the win.
“We created lots of chances and didn’t quite take them but we went all the way to the whistle.
“Coming here a getting a point would have been a good result but we’re not happy with that as a squad and that’s our mentality.
“We have a squad of game changers and quality, experience and real pedigree.
“Leyton Orient are a very good side and Richie Wellens has done a magnificent job here. So to come here and play the way we did, I was very proud.
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