The spectacular 2-2 draw at the Stadio Dall'Ara was marred by a controversial performance from referee Gianluca Rocchi.
"Looking back at the footage, Clarence Seedorf did seem to handle in the box, but towards the end there was an identical handball not awarded for us," said Allegri.
This was the Rossoneri's second consecutive 2-2 draw after a midweek stalemate with Viktoria Plzen in the Champions League.
"After taking the lead we defended badly and couldn't even hold on to it for a minute. Our second half was not up to the task, even if we had a few good chances towards the end.
"We didn't throw any points away here, though, as Bologna played very well to earn the result with real determination. Marco Di Vaio was excellent at moving between the centre-backs and Bologna were very rapid on the counter-attack.
"Milan made mistakes and we paid for them."