Fleetwood boss Micky Mellon felt Barnet 'keeper 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."