Two goals in four second-half minutes from Anthony Wordsworth and Freddie Sears gave the U's victory and ended their run of three straight defeats.
Blackwell said: "Fair play to Colchester - they dug in when they needed to and they got the clean sheet as well. Their keeper made two good saves and came and got some crucial crosses.
"We came out after half-time as the dominant side, but we gave them their first goal after we had possession of the ball.
"There's no need to do what he's done and we gave away a stupid goal and that gave them a lift, which was all that they needed. It just shows you that if you play in the wrong areas, that's exactly what can happen.
"We were the better team after half-time and we knew we had to stop Colchester playing in certain areas, which we sorted out. We'd have come here three weeks ago and got battered."