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John Filan was ruled to have brought down substitute Simon Atangana in the 90th minute of Saturday's clash.
The assistant on the far side of the pitch signalled for the penalty although contact between the goalkeeper and striker looked minimal.
With Filan appearing to be the last man, Jewell had sub keeper Dave Beasant ready on the touchline should he have been sent-off.
But Mr Penn felt there had been cover behind Filan and let him off with just a booking.
Joe Keith converted the spot-kick to reduce the arrears after Jason de Vos and Andy Liddell's penalty had put Latics in the driving seat.
At the end of the match, Jewell raced straight to Filan to give him a pat on the back and make sure he didn't continue his protests.
And with his keeper safely heading for the tunnel, the manager then turned his attention to Mr Penn.
Jewell said: "My main concern at the end was to get John away from the referee.
"I thought he would have sent him off when he awarded the penalty.
"At the end, I asked the ref to look at it again, although he can't change his mind now.
"Had he sent John off, we would have lodged an appeal and we would have won it.
"Referees have a difficult job and it was actually his linesman who gave it. His assistant is there to help him, he went over to have a chat about the penalty, but obviously it was the wrong decision.
"There were four minutes injury time after that, and I'm just delighted we got through."
The win was Latics' 11th in the league on the spin and stretched their unbeaten run to 21 games.
But Jewell admitted his side had made hard work of securing the points against their lowly opponents.
He said: "The display wasn't very good although you have to give the players credit because they have won the game.
"Teams will come here to sit deep and make life difficult for us and I thought Colchester held us comfortably in the first half.
"Jason's goal just before the interval made the half-time team talk much easier – it was a great ball from Gary Teale and Jason really made it his.
"We knew we weren't at the races, there wasn't a great atmosphere again and we had to struggle through it.
"The second half was much improved. We created more chances, but nothing like we can do.
"But it is all about getting victories at this stage and that is what we have done."
The penalty for Latics' second goal had a touch of controversy about it too, de Vos seemingly blocked by defender Alan White at a free-kick.
Jewell said: "That happens all the time. The ref had a word with their players just before it happened and there didn't seem to be too much argument from them.
"But there is push and shove all the time, and if that's the case, there would be 20 penalties every game."
Article from the Wigan Evening Post.