Carroll tormented the visitors' defence with his physicality and aerial prowess for the best part of an hour, assisting both of Kevin Nolan's goals before he clashed with Flores.
The Spaniard went down clutching his face after being caught by Carroll's flailing arm, though replays suggested only the top of his head was grazed, and Howard Webb produced his red card.
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"I don't think you can say it's a ridiculous decision because it's the reaction of the player that makes life extremely difficult for the referee," the Hammers boss told reporters.
"So while I think it's harsh I can see why it was given. He must have thought the arm has smashed him in the face when it hasn't.
"All I can hope is the panel see it for what it is. Andy is gutted. He's absolutely beside himself. But that aside we just have to go through the process and see what happens.
"We don't have a player like that. None of our players attempted anything like that.
"If anyone could have done anything remotely like Chico Flores did it would have been Matt Jarvis when he went round the goalkeeper.
"If he'd left his leg out like most do and let it catch the keeper and gone over, he could have got a penalty and the keeper sent off. But he didn't - he went round him and tried to score a goal.
"In the end it hasn't cost us anything because we were saved by the brilliant 21st century defending by the players - Swansea didn't have a shot on target all game."
Swansea boss Michael Laudrup sympathised with Carroll and admitted he was not aware whether Flores had cynically tried to influence Webb's decision with his reaction.
"It was a bit harsh," the Dane admitted. "My personal opinion was that it was contact without much more.
"I don't know if he wanted to get Carroll sent off. I'll have to talk to him about what his intention was.
"But the referee is a very good international, so he must have seen that elbow from Carroll and judged he did it on purpose. As far as I know the rules are that if there's intent it's enough [for a red card]."