Hughes had previously seen Bulgarian striker Valeri Bojinov hobble off the field during the warm up, to be replaced by Ched Evans.
On the injury, Hughes said: "It's a huge blow to Valeri and to the team, just prior to kick off. The likelihood is that he is going to be out for six months as he has ruptured his right Achilles tendon. It's a terrible blow for him after the injury worries he has had over the last 12 months, he did really well to come back and he deserved his place in the team today."
The former Wales boss felt the scoreline was an unfair reflection of the performance. He told the club's official web site.
"I thought we were well in the game, and when we got back on level terms I felt that we were in the ascendancy and that we were going to go on from that.
"Unfortunately we invited pressure on ourselves, made poor decisions in key areas and were not able to recover. All the hard work evaporated in those eight minutes, and the game went away from us."
"I think people saw an improvement (from Thursday's Uefa Cup defeat). You have to sustain a performance from the first minute to the last, we didn't so for an eight minute spell and it has cost us the game. That's the level we play at, you are up against good strikers and a lapse will cost you.
"I don't think the scoreline is a reflection on how we played, it hurts at the moment but we will pick ourselves up for a big game next weekend. Unfortunately everybody is flying off for internationals, but we will get the group back on Thursday and work on the issues that came out of today.
"I'm not going to criticise individuals, we were in the game for long periods and I saw a lot of things I was happy with," he concluded.