The U's slipped to defeat with two goals in three second half minutes from Hartlepool United, after Noah Chilvers had put his side ahead at the break.
The U's headed into the break with a deserved lead after Noah Chilvers had capitalised on Ben Killip's spillage, with the home side also striking the woodwork in the first half.
And Colchester United hit the post for a second time during the game just a minute into the second period.
But the hosts were unable to build on their lead as Hartlepool United turned the game around in three second-half minutes with Bogle and Fletcher both on target.
Wayne Brown made four changes to the starting eleven from the defeated side at Northampton, with Judge, Eastman, Tchamadeu and Huws all missing out.
Taking their places were Brendan Wiredu, Noah Chilvers, John Akinde and Cam Coxe.
In the opening fifteen minutes, there were a couple of half chances for either side, with Freddie Sears flashing an effort just wide of Killip's upright, and White slicing the ball over Hornby's bar at the other end from a free kick.
But twenty minutes in, the first real effort came, and it fell to Noah Chilvers who obliged in smashing the ball home after the visiting 'keeper's parry. Killip was unable to hold Akinde's shot from close range, with Chilvers rifling into the back of the net from the six-yard line.
Wayne Brown's side kept the pressure up on the visiting defence, and were unlucky not to have added to their tally ten minutes later. John Akinde picked out the bursting run of Cameron Coxe, who drove towards goal before cutting in and unleashing an effort that bounced off the foot of the post and out for a goal kick.
The visitors were limited in their chances at the other end of the pitch, with a penalty appeal from Luke Molyneux falling on deaf ears, as well as an alert Sam Hornby denying Bogle's effort from the edge of the eighteen-yard box.
But the U's were good value for their half-time advantage, and lead Hartlepool United by a goal-to-nil at the mid-way point in the game.
Not a minute of the second half had elapsed when the U's struck the woodwork for the second time in the game. This time it was Freddie Sears getting on the end of Coxe's parried cross, with the U's top scorer putting the ball through the legs of the Hartlepool 'keeper and against the foot of the upright.
And five minutes later, the visitors had their own effort striking the frame of the goal. Omar Bogle struck a powerful effort from the edge of the penalty area that took a deflection before crashing against the top of the crossbar and out for a corner kick.
Bogle did get his goal fifteen minutes later, after a quick break from the visitors. The forward was picked out on the far side, before cutting in and firing a powerful shot low beyond Hornby and into the bottom corner to level the game.
The visitors completed their turnaround three minutes later when Isaac Fletcher had come off the bench to give his side the lead. Bogle was the key man for the visitors again, twisting and turning inside the U's penalty area, before sliding the ball to the substitute who slotted low beyond Hornby and into the back of the net.
Wayne Brown's side caused a handful of late issues for the travelling defence, but Hartlepool were able to deal with whatever was thrown at them as they held out to take maximum points from the game.
The defeat means the U's remain in twenty-first position with thirty-one points from thirty-two games.
Up next is another home game, with Oldham Athletic, the team directly below the U's in the table, visiting the JobServe Community Stadium on Saturday afternoon.
Colchester United starting XI: Hornby, Chambers, Smith, Wiredu, Skuse, Sears, Edwards, Chilvers (Wright 87'), Kenlock, Akinde (Andrews 60'), Coxe.
Unused subs: George, Judge, Dallison, Tchamadeu, Huws, Wright.
Hartlepool United starting XI: Killip, Ferguson, Odusina, Shelton (Fletcher 65'), Bogle, Featherstone, Molyneux (Carver 78'), Byrne, Crawford, Francis-Angol (Smith 77'), White.
Unused subs: Liddle, Holohan, Hull, Bilokapic.