Cotterill claimed that decisions by the match official had cost his side dear as goals from Seyi Olofinjana, Jay Bothroyd and Peter Whittingham condemned them to defeat.
The Pompey boss took issue with the 18th-minute red card handed out to Ricardo Rocha after he clashed with Bothroyd. And he felt that the free-kick that led to the hosts' second goal was a contentious call that put his side on the backfoot.
Cotterill said: "It probably changed the game when we had a player sent off because I felt we were well into the game at that point.
"I don't want to make any excuses as I haven't seen the incident on video but our player has a gash on the side of his face. And I don't know whether Bothroyd should also have been sent off.
"We have been on the back end of some poor refereeing decisions and it wasn't even a free-kick before they scored their second goal."