Bolton boss Owen Coyle rounded on Zat Knight for the mistake which secured a 2-0 win for Stoke.
The Potters were leading through Danny Higginbotham when Knight floored Matt Etherington in the area and the winger tucked in the penalty which effectively put the match out of sight.
Coyle said: "It was a poor penalty for us to give away. Zat Knight has been outstanding but he knows he should have stayed up.
"Etherington was on his weaker foot and sometimes you have to recognise these situations. Jussi Jaaskelainen nearly saved the penalty but we found ourselves 2-0 down.
"We kept going forward and getting in dangerous positions but their keeper made a couple of good saves and we couldn't get that elusive goal to get us back in the game."