Shrimpers substitute Barry Corr salvaged a share of the spoils for the Shrimpers when he headed home five minutes from time at Roots Hall.
But Brown was still left frustrated by his side's display, and he said: "I was disappointed with how we played and too many of the team wanted to pass it on and let someone else make things happen.
"Against Bradford on Friday we had seven or eight players who put themselves forward for a starting slot at Wembley in this weekend's JPT final with Crewe but there were far fewer than that out there.
"We started off with a 4-3-3 formation and I decided to include Freddy Eastwood as he's a talisman here at Southend. However, it didn't really work and I thought we lacked width. It was only when Barry Corr and Marc Laird came on that we started to play well but we were still reliant on our goalkeeper having to make a couple of good saves."
Brown's first match since taking over from Paul Sturrock ended in a 2-2 draw at Bradford City on Friday. But it was Fleetwood who started the stronger and they took the lead after just two minutes when Alan Goodall headed home Junior Brown's right wing corner.
Fleetwood midfielder Gareth Evans then had a 37th-minute penalty saved by Shrimpers goalkeeper Paul Smith after Ryan Cresswell was adjudged to handled the ball.
Southend made the most of the let off in the 85th minute when Corr headed home a left-wing cross from Britt Assombalonga. However, Fleetwood still came close to winning it at the death when Barry Nicholson had a low shot tipped around by Smith. And Town boss Graham Alexander was annoyed his side were unable to secure all three points.
"I'm disappointed to draw the game because I thought we were in control for most of it," he said. "But playing two games in three days really hit us hard and that showed in the last half hour of the match when Southend found their way back into the game.
"Paul Smith made a great save to keep the penalty out in the first half which obviously proved costly in the end but everyone worked their socks off and we just didn't have the energy levels at the end as the fixture list hasn't done us any favours."