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Ulster were edged out 19-15 as Clermont stretched their unbeaten home run to approaching 40 games in an enthralling encounter that could have gone either way.
The visitors, who have qualified for the last eight as one of the two best runners up, led on two separate occasions in the second-half before a solitary Clermont try swung things their way.
And McLaughlin, who watched his men trounce former champions Leicester Tigers 41-7 last weekend, admitted things could have been different had his team been a little more clinical in either half.
"We're bitterly disappointed with the result. We came so close. We came here wanting to get a home quarter-final for our fans and that's why we're exceptionally disappointed," said McLaughlin.
"In the first half we missed a couple of penalties - difficult though they were - and we had a couple of try-scoring opportunities that we left out there. When you're playing in a brilliant competition like this, you just can't afford to do that - you've got to take every opportunity that comes your way.
"We finished the game on the attack, going for a try, but then lost the last lineout. These are things that you just have to get right at this level. You've got to be ruthless and that's something we'll have to learn."
There were plenty of positives to take from a pulsating 80 minutes, however, and McLaughlin was clearly a very proud man after Ulster really rattled the partisan home support.
The 1999 Heineken Cup winners showed that a repeat of that famous triumph in May 2012 is a real possibility and no one will be taking Ulster lightly come quarter-final time.
"We came here with high hopes and full of confidence and I'm very proud of what this Ulster squad did on the day," said McLaughlin.
"I was really pleased with the way we competed and the way we took the sting out of Clermont when they were running everything in the first 20 minutes. Our set scrum was good; we showed that we can create chances; and our collisions and our work in the contact area have improved immensely.
"We're in a quarter-final and we backed up what we did last week. We wanted to show that we're proper contenders in this competition, that we can be talked about in the same breath as Leinster, Munster and Toulouse, and I felt we did that."
