The 'Blues' scored three late goals to secure a stunning 3-2 victory over Southampton in the Premier League's early kick-off.
However, that wasn't the biggest talking point of the game. Alonso caught Long on the back of the leg with his studs after a late challenge which was missed by match official Mike Dean.
Speaking after the game, Hughes was baffled by the decision: "Shane's got a gash down the calf, having seen it again there's a clear red card. There's clear intent to hurt Shane, it was raked down the back of the calf.
"It's a dangerous tackle and could have broken his leg, in my view, and how the three officials who were near it all missed it was a mystery to me."
Turning his attention to the result, Hughes admitted that time is running out for Southampton, who are three points from safety in 18th with just five games remaining.
"You've seen in the last two games, against Arsenal and Chelsea, I've seen encouraging things but other things that will damage us in the games we've got left unless we improve.
"But I've got a willing group, one that is fighting to turn this round, I'm pleased up to a point but we've not taken anything out of a game we should have won.
He continued: "For the most part I was pleased with what I was seeing, I saw a team that was committed to what we are trying to do.
"That was evident and we got ourselves into a great position, a winning position because we should have seen the game out, but we've got a soft underbelly which we've had all year apparently."