United won 2-1 after extra-time at the Liberty Stadium, but the main talking points were the three sending offs of Swans players and the referee's decision to bring an injured player back onto the pitch to avoid the game being abandoned.
Garry Monk, Gorka Pintado and Angel Rangel were all sent to the dressing room by James Linnington.
Injuries to Stephen Dobbie and Besian Idrizaj looked set to force the game to be abandoned, but Linnington made Idrizaj play out the game.
"I never wanted the match abandoned but Idrizaj should not have gone back on the field but as we were then down to only six players the referee put pressure on us to get him back on," said Paulo Sousa, the Swansea manager.
"We have been provoked and we have reacted not in a good way but my way is to protect my players. We have our opportunity to write to the FA about the referee's performance but at this moment we do not know what offences the players have committed."
Adkins was happy his side kept their composure enough to seal progression intot he third round of the competition - a fine way to bounce back from the disappointing 4-0 loss at Sheffield Wednesday on Saturday.
"Swansea's lack of discipline has cost them dearly as they are an excellent side. They are a fantastic passing team and we are really pleased that we defended well against them," he said.
"The discipline of my players was also very pleasing and the referee had no choice but to send their players off as they seemed to lose their composure."