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Ryan Jackson was sent off on Saturday but Gillingham manager Steve Evans felt Southend should have had a man dismissed too.
Jackson picked up two bookings for fouls - the second which Evans had no issue with - but he was left baffled when Southend captain John White got away with a second one himself.
"The referee didn’t have a good game,” said Evans, speaking about man in the middle Christopher Pollard.
“It made it harder for us, but all you ask if that the referee is not seen on the pitch. He (should) make the same decision for both.
“I understand the decision for Jacko’s second booking, no complaints, I said to the staff straight away ‘he’s gone’. I saw it happen to the other team and it doesn’t happen, it is mystifying.
“The Southend player was already on a yellow. He absolutely smashed Stuart O’Keefe and nothing happens.”
It was Jackson’s first competitive return to Priestfield after making a summer move, returning to the club where he made 71 league appearances for the Gills between 2015 and 2017.
His second foul, on 58 minutes, saw him take down Southend's Jordan Green.
But the first challenge, a 40th minute coming together with Isaac Hutchinson wasn't so clear-cut.
Evans said: "The first one is a mystery. He waves play on, the fourth official brings it back and then the referee books him. That’s strange."
More on Saturday's game;
Report: Gillingham 1 Southend United 0