The match ended in a 2-2 draw but in the final 10 minutes, referee Lucy Oliver brandished a second yellow to Green but failed to send her off.
Everton boss Willie Kirk was left "baffled" by the decision as his side remain in second position in the table, two points behind leaders Arsenal.
"We have to talk about it, that's a major incident," Kirk told BBC Sport. "For a player to be booked twice and still be on the pitch is baffling.
"I think it's only happened once in my lifetime. It shouldn't happen. Nobody wants players to get sent off but that's how the game goes.
"It would have given us an opportunity to really get at them in the last 10 minutes. It's frustrating the referee made that mistake."
"I wasn't sure [what happened]," Brighton boss Hope Powell said after the match. "I said to the fourth official: 'She couldn't have given her a yellow?' He said she had. So the referee has to be in control of that.
"It's hard for me to comment because you will have to ask the referee if she gave a second yellow card as I don't know. The fact that she was on the pitch? I don't know.
"For us, the gods were on our side today. If she did get a second yellow then I am sure, if I was Everton, I wouldn't be pleased about that."
Earlier this year, there was another mix-up in the men's game when a non-league footballer was shown three cards in the space of 12 seconds.