Colchester manager John Ward spoke of his disappointment at conceding the late goal to Carlisle which denied his side first place.
Paul Thirlwell swept home in the third minute of injury time from close range after Gary Madine had fired the ball into a crowded area to earn his side a 1-1 draw.
Colchester were the better side in the first half and took the lead just before the half-hour mark. Brian Wilson's deep cross was headed in convincingly from close range by on-loan striker David Mooney for his first league goal for the U's.
Ward said: "I can't really deny them their equaliser. I was hoping we could see it all the way through but we didn't and I'm sure even the most partisan Colchester supporter - and that includes me - can't really deny Carlisle taking a point back with them.
"That's how it is and the players have put a fantastic effort in. They've had a huge week with trips to Rochdale and Sunderland. It's no excuse but it's been a big week and we've had a fantastic effort again.
"The boys are so upset and deflated but we've come to the end of August and we're unbeaten. That's how hard it is to get to the top of this league. We'll try and learn our lessons and pick ourselves up and go up to Walsall. If we can win at Walsall, we can get smiling again. It was a fantastic effort in a real top-of-the-table game."