The performance left Megson angry, with the manager saying: "You can't defend at any level - never mind this one - like that at all.
"It was not a case of defending badly as a unit, ie: the back four; individually we have made three errors that have cost us and we also made a couple of errors which we got away with.
"Defensively we really poor. I feel only Gary Cahill has performed anything like what I would expect - he was okay without being brilliant.
"But I thought a lot of our players, in terms of getting hold of it and passing it, were poor and also the tempo was not what we needed."
Megson felt two of his more experienced players in O'Brien and McCann should have dealt better with their situations.
"We can't do anything about it now. Making a mistake happens but making it twice - I can't accept that," said the Bolton boss, whose side are just four points above the bottom three.
"Each of the three goals wouldn't have happened if we had cleared our lines.
"I have spoken to them (O'Brien and McCann) and we need to put a line under it.
"It is a bit galling to get to this stage of the season and have to revisit what we should be doing with experienced players.
"Andy has made one or two mistakes - so has everyone - but today they have been highlighted because they have cost us goals.
"But he is a terrific lad and is a great pro but he has played poorly today - quite a few have - but Andy will hold his hand up.
"We are all culpable and there is only Gary can honestly come out and say he did okay. It was a poor day for us right the way through."
In the 42nd minute O'Brien poked the ball past his own goalkeeper Jussi Jaaskelainen and saw Andrew Johnson slide in at the far post to score.
Kevin Davies equalised in first-half injury time but 11 minutes after the interval another mistake by O'Brien allowed Johnson and Danny Murphy to set up Simon Davies to add a second.
Fulham substitute Diomansy Kamara added a late third after McCann's aimless ball into midfield was punished.
It was the Cottagers' first away win since the final day of last season and came after back-to-back home defeats.
"I'm happy with the result and the performance, I thought we played very well," said manager Roy Hodgson, whose team are now eight points clear of the relegation zone.
"I've been a little bit unhappy with the last two results, although not the last two performances.
"When we conceded a goal in injury time I was rather concerned the players would not be able to pick themselves up and give the same performance in the second half which had given us the lead in the first but luckily they did."