Sousa stunned with penalty error
The match was level at 0-0 when Angel Rangel appeared to foul substitute Giles Barnes but replays have shown it was a dive. Graham Dorrans converted the 79th-minute spot-kick before Ishmael Miller added a second as the Swans threw men forward in search of a leveller.
Paulo told the official site: 'From my line of view, I thought the referee was going to give a yellow card to the player (Barnes) because he dived. After seeing it from different angles, I'm right.
'The referee saw it differently, but it's something we are used to. It's the first time I've gone into the referee's room after a game. We spoke like adults, but it didn't make any difference.
'I've spoken so many times about the referees and decisions and I have my point of view about these things. Perhaps as a club we will consider sending a DVD of all the incidents over the season to the English FA and Uefa. We'll think about it.
'When I complain, it's only for the game of football because referees play an important part.
'I like a lot of respect for the work of my players, myself and the club. The players deserve respect.'
As for the game itself, Paulo said: 'We started really well. We dominated and put them under a lot of pressure.
'In the second-half they changed their team and brought on power and explosion up front which created us a lot of difficulties. They closed a lot of our space down and the game became more balanced. It looked like ending 0-0 until the penalty incident.
'But we need to be strong now for the rest of the season and we can't afford to look back on all these decisions going against us.'