The Welsh side battled back from two goals down to lead 3-2, with Wilfried Bony scoring his second in the 86th minute.
"I'm so frustrated, we have experience that teams score against us in injury time," the Dane told Sky Sports News.
"What is incredible there is always opinion about 'is it a penalty, it is not a penalty' - but how on earth can you explain that seven Stoke players inside [the box], none of them are asking for the penalty and still the referee gives it in the 94th minute?
"I don't have words. It's really incredible."
By conceding late on, the Swans missed the chance to go 10th in the table.