The visitors scored all of their goals in a one-sided opening half, and although City pulled one back after the break, McInnes admitted they were still second best in all departments.
"We lost the physical battles and it was a very poor performance," said the Robins boss. "It was on the back of two decent away displays and I didn't see it coming.
"We never got to grips with the Wolves front two all game and our fans are entitled to be upset.
"Being booed off is never nice, but I can understand their feelings. After we lost the first goal we capitulated and Wolves grew in confidence.
"Even though we won the second half, as I asked the lads to do at half-time, Wolves had more chances.
"The goals we gave away were awful. Wolves were stronger than us all over the park and that was a major factor."