The Potters took the lead through Charlie Adam after 26 minutes at a sunny Selhurst Park, before a second-half brace from Dwight Gayle saw the Eagles come back to claim victory.
The defeat leaves Stoke without a win in their last six games, with Hughes admitting he was disappointed by the way his side performed after the break.
However, the Welshman insists his side were not done any favours by the performance of Friend, whose decision to hand the hosts a second-half free-kick allowed Gayle to step up and curl home the winner from 25 yards.
He told Sky Sports after the game: "We got ourselves into a winning position and I thought we were good value in the first half. In the second half we came out and conceded almost immediately and gave them a little encouragement.
"It [the first goal] was poor defensively from our point of view, we missed three or four tackles leading up to the goal, which should have been cut out before the lad [Gayle] was able to get the shot off and score.
"Then we're obviously penalised on the edge of the box, which was a poor decision by the referee and was one of many from him unfortunately."
"I don't think we deserved to lose the game. I think a draw was probably a fair result on a day when both teams didn't really produce a high-quality game."
Despite their difficult recent run, which has sparked accusations that the players have already cast their mind forward to next season, Stoke can still seal a third consecutive top 10 finish with a win over West Ham United on the last day of the season.