Fleetwood boss Graham Alexander lamented the decision to award Southend a penalty in their 2-0 loss at Roots Hall.
Barry Corr scored both goals and it was the second, which came from the penalty spot in the 81st minute, which angered Alexander.
The Irishman sent his 12-yard shot high in to the left-hand side of the goal after Will Atkinson had been brought down by Liam Hogan.
"We've conceded a poor goal in the first half which put us on the back foot but we had some really good chances that we didn't take," said Alexander.
"We tried to press Southend but didn't have enough quality around the box.
"We responded well to going behind and passed the ball well but couldn't find the end product.
"We have a great team here and you take bumps and bruises on the way and we just have to take it on the chin.
"But I'm adamant that the Hogan won the ball when the referee gave a penalty, I have watched it back on video and it wasn't a penalty."