Ryan Leonard headed the visitors into the lead before the Shrimps levelled after 29 minutes through Kevin Ellison, with second-half substitute Jack Redshaw proving the hosts' matchwinner courtesy of a superb finish with his first touch of the ball.
Brown said: "We started superbly and got an excellent goal but we didn't take advantage of that.
"We gave away a really sloppy goal to let them back in the game and we never recovered. It really took the stuffing out of us.
"We were poor in the second half and their second goal was another killer because it came just seconds after we could have scored.
"Morecambe had too much nous for us at the end of the day and we have to learn that we can't play pretty football all the time, especially on a pitch as poor as this one.
"Morecambe played the conditions the better and that proved to be the difference."