However, the former Sunderland boss did take some positives out of the match and was particularly pleased with the performance of Hoolahan in midfield.
"I thought little Hoolahan played brilliantly for us. He tried to create things for us during the course of the game," O'Neill told reporters.
"Sometimes some big boots come in and shove him off the ball a little bit, but overall he showed a great determination and great ability to try to manoeuvre it. He was excellent for us."
Ireland's next match comes on Saturday as they face Italy at Craven Cottage.