Fleetwood boss Micky Mellon believes Barnet goalkeeper Graham Stack's sending off hindered rather than helped his side in the 2-1 win.
The Bees were leading 1-0, courtesy of Jake Hyde's fifth-minute opener, when Stack was given his marching orders for upending David Ball in the box in the 24th minute.
Ball converted the penalty before on-loan Blackpool midfielder Tom Barkhuizen headed in the winner for Fleetwood.
It is the second time a visiting team have been reduced to 10 men in the first half against the Cod Army this season and Mellon insists it does not make life easier for his team.
He said: "That happening so early in the game has pluses and minuses. It's very difficult against 10 men. You have to be very, very patient and take chances when you get them.
"We got ourselves in some great positions, maybe the final ball was lacking, but we're delighted with our victory. We were disappointed with the early goal because we knew about that and had practised that free-kick on Friday.
"Thankfully we were able to come back from that."
Bees boss Mark Robson labelled the penalty decision as the game's turning point.
He said: "The lads weren't sure if it was offside or not. If that's given offside then it's a free-kick to us. As it is, he's got in, the lad's brought him down and the rules are that Stack has to go. It's a major disappointment.
"We started well after putting in a really good performance last weekend and really thought we could get something out of the game. I felt we were just starting to come together, unfortunately we lose a man after 25 minutes and it's all happened from there."