Birmingham City were angered that goalkeeper Hannah Hampton was left “in floods of tears” after being told she was not shortlisted for Great Britain’s Olympic squad just 90 minutes before Thursday’s WSL game against Everton.
Blues boss Carla Ward said Hampton, 20, needed consoling during the warm-up.
Ward said the timing was “unacceptable” and it “clearly affected” Hampton in the 4-0 defeat.
The Football Association apologised and said the timing “was an error”.
A spokesperson for the governing body continued: “We take full responsibility for the upset this has caused.”
Watching Hampton struggle emotionally and make a series of errors during the defeat prompted Ward to speak out against how the FA chose to relay the news to players.
“We have a big welfare issue in terms of looking after her,” Ward said. “We will pick her up, support her in the best way we can.
“We spent 45 minutes with her and she was deeply upset. Our focus should have been on the game and her focus should have been on the game.
“We didn’t know if we were playing her or not. Everybody saw a Hannah Hampton performance which isn’t Hannah Hampton-esque.”
Players from both sides were told whether or not they had made the squad before the game, but Ward said that did not excuse how the announcement was handled.
“You wouldn’t get it happening before Champions League tie but it’s OK to deliver news to both sides an hour and a half before kick-off when it’s Birmingham v Everton,” Ward said.
Everton manager Willie Kirk, who had two players told they were selected and two others informed they were left out, agreed that communication “was very poor”.
“A player finding out that news two hours before kick-off is wrong,” Kirk said.
“It’s important if you’re sharing good news or bad news that the clubs get a heads-up so they can try to support that.
“It has affected our players and I think the players it affected have dealt with it very professionally tonight and both put in good performances.”
Bradley Rains, agent and head of women’s football at Coda Independent Sports, represents several players who are believed to have been considered for Team GB, including Hampton.
He told BBC Sport: “Of course anyone would be hugely disappointed to miss out on an Olympics. But the timing of this message just before an important league game is extremely unprofessional and ill-judged.
“To deliver news in this manner and timeframe to valued members of the home nation squads and domestic leagues leaves a bad taste.”