Salop fell to a 2-0 defeat at Portman Road as The Tractors Boys scored a goal in each half to condemn Town to defeat in front of more than 25,000 fans.
George Hirst gave the hosts the lead in the 15th minute by heading home Wes Burns' cross, and Massimo Luongo doubled their advantage after the break.
And Cotterill was left frustrated after the game with the way Ipswich scored against his Town side.
"Two poor goals, we are disappointed with the goals we have given away and the manner of them," the Town boss said.
"The players always give it their all, but we cannot afford to have a couple of lads missing.
"Today we could have done with Killian, we could have done with Tom Bayliss and we could have needed them in our midfielder which would have helped us - certainly as the game went on.
"A few of our lads could have played a bit better than they did, and I think Ipswich are probably the strongest team that we have played this season.
"They are really too big a club to be in League One so we knew it was going to be difficult to compete when you come to places like this.
"But all in all the lads give what they can.
"It is always disappointing to concede a goal, we were disappointed with how we defended both goals.
"They were both preventable, there is nothing new there, and it is not something we have not already spoken about this week.
"But sometimes you come up against a team, and there is nothing you can do.
"We are very very light, and we have done it all season, and we have pushed it and pushed and pushed it as far as we can.
"When you come up against sides like this, they can put five subs on, and they would probably get into our starting line-up, and it is a fantastic luxury.
"The challenge for Ipswich is not getting up it is when they get up, it is competing with those teams who are up. That will be the challenge.
"A very difficult day."