In-form Brentford were in cruise control early on after goals from Marcello Trotta and Adam Forshaw had given them a two-goal lead and Colchester defender Josh Thompson was sent off for a professional foul.
But U's teenager Drey Wright gave Colchester hope and Brentford had to rely on Harlee Dean's late goal to extend their unbeaten league run to 10 matches.
Dunne said: "There were lots of positives to come out of the game and we were brave, but we didn't get anything out of it and we're judged on results.
"The application after the first 10 minutes was excellent, but basic errors cost us again.
"When the ball comes into the area, we have to be able to defend it better overall, there were a lot of positives to take.
"Drey Wright was outstanding - he had an exceptional debut and really showed his strength and all of the young players who played for us showed great courage.
"In our previous two games we'd been a bit tighter and I've taken a bit of stick for it, so we went and attacked them.
"Unfortunately, we were chasing the game again and we don't seem to have the balance between attacking well and defending well.
"Two of the three goals that we conceded were basic goals."