Clough said: "The penalty was one of those where sometimes you get them, sometimes you don't.
"Harry Maguire appealed straight away and the linesman was only 10 or 15 yards away, so it must have been pretty clear.
"It was nice that after going two-up in a great opening period that we didn't sit back.
"We conceded the two goals, probably through a bit of naivety, we were probably a bit too far forward, but we eventually got the win that we deserved.
"We told the players at half-time that when you are so much on top and the home side are under pressure, you have to get as many goals as you can and a third would've killed them off.
"But they probably got a rollicking at half-time, it all changed and it was a good cup tie - we still had the far better chances in the second half."
Furious U's boss Joe Dunne said: "I have seen it again and it's an appalling decision that's cost us.
"Magnus was about one yard away and he has no reaction time to make a deliberate decision to block that ball - it's impossible for him to get away from it.
The Blades struck twice in the space of two first-half minutes to take a 2-0 lead.
Maguire headed in Tony McMahon's free-kick in the 10th minute before Porter closed down Magnus Okuonghae's pass and delivered a cross-shot which flicked in off Tom Eastman.
Matt Hill struck the crossbar for the visitors, but Colchester reduced the deficit three minutes after half-time through Macauley Bonne, after Clinton Morrison had flicked on Luke Garbutt's delivery.
And Garbutt drove in a superb 25-yard shot from Brian Wilson's throw to equalise just after the hour-mark before Porter's controversial penalty sent the Blades through.
- Sports & Recreation
- Magnus Okuonghae
- Harry Maguire
- Chris Porter