The Robins dominated the first half and had enough chances to beat their fellow strugglers but instead had to settle for a point which leaves them in the bottom two of the npower Championship.
To add to City's misery, their relegation rivals Barnsley, Sheffield Wednesday and Peterborough all recorded victories.
McInnes said: "I'm frustrated not to get three points because I thought we were by far the better team.
"When you play that well and create chances, you hope to win.
"We dominated the first half, although the second was more even, and played with a confidence.
"There was a concentration and focus about us, which is especially important in away matches."
City took the lead in the 11th minute through a fine strike from Neil Danns but that advantage was cancelled out in the 32nd minute when Tommy Smith acrobatically drew Ipswich level.
"We knew it was going to be a tough afternoon but I thought it was even tougher for Ipswich," said McInnes.