Mark Davies' long-range effort gave Wanderers a flying start but they failed to add to their lead and DJ Campbell levelled with a 70th-minute penalty before Michael Chopra netted a last-gasp winner for Town after a handling error by Adam Bogdan.
"Ipswich thoroughly deserved to win the match and we've got no complaints," Freedman said.
"I felt for 70 minutes we played very well and were the better team because we were creating opportunities. We probably actually did enough to win the match.
"We didn't take those chances though, and in the last 15 minutes we were a bit edgy.
"That gave them the impetus and the chance to make us pay and they did that to us in the end."
Speaking about the performance of goalkeeper Bogdan, Freedman added: "In football there are so many ups and downs and Adam has had so many of those ups recently.
"It was a difficult shot to stop and I thought that he was one of our better players overall and I think the message is that we've got to see our games out."