What was an excellent performance by Villa was overshadowed in some part by sickening chants from the visiting section about injured Arsenal striker Eduardo.
The home fans were clearly incensed, and there were reports of scuffles outside the stadium.
O'Neill commented: "If that is true, then I am desperately disappointed by that."
Wenger, meanwhile, was less graceful. The Arsenal boss said: "You expect better from people who come to stadiums.
"I don't know what to say. Intelligence and stupidity can have no limits."