Fans clashed on the Ibrox pitch after Celtic knocked Rangers out of the Scottish Cup on penalties on Sunday.
The Hoops progressed to the semifinals despite failing to register a single shot on target in 120 minutes of action.
Celtic secured a 4-2 shoot-out victory after the goalless draw before dozens of their fans invaded the pitch. That sparked an invasion from hundreds of Rangers supporters and missiles were thrown as police and stewards moved to form a barrier.
Police officers apprehended a man after Celtic players, including Tomas Cvancara, ran to the scene amid an incident involving a Celtic member of staff.
Cvancara, who scored the winning penalty in the shoot-out, was later interviewed on Premier Sports with blood stains on his strip.
Flares were thrown and some minor skirmishes appeared to take place before order was restored and the 7,500 Celtic fans were left to celebrate alone.
Asked about the altercation between a spectator and one of his staff, O'Neill said: "As we were making our way back, I think there was some sort of fracas; somebody tried to get on the field. I don't know, all I saw was there was a bit of a scrum down at the bottom.
"And as you say, maybe it does taint proceedings, but I think there's an element of self-protection in that one. So if that's the case, please, I'm making judgments here on things that I only half saw."
O'Neill added: "The security men, in fairness to them, were wanting to get people off. But there is a natural euphoria about winning a game and about fans joining in. If this has gone too far, that would be disappointing."
When asked if he had spoken to the players about the incidents, O'Neill said: "I just said well done to the team and I went into my own little room to cool down myself. My heart's beating at a rate that a 74-year-old's shouldn't be doing."
Rangers head coach Danny Rohl said of the trouble: "I was not on the pitch in this moment. I didn't see it until now. I heard just that there was something on the pitch.
"I think we all know the emotional situation after a game. Nobody likes to see this. I think it was a great atmosphere, 120 minutes. I think it should be like this. All the other things should not be in the stadium or around football."
Scottish football reacts
The post-match clashes have been branded a "disgrace" and "an embarrassment for Scottish football" by the Scottish Football Association and the country's governing body has confirmed that an investigation into the incident has been launched.
A statement read: "The Scottish FA condemns the behaviour from supporters entering the field of play following today's Scottish Gas Scottish Cup quarterfinal at Ibrox Stadium.
"An investigation will be carried out immediately in line with the Judicial Panel Protocol."
Meanwhile, former Scotland international Charlie Adam, described the scenes as "a disgrace."
Speaking on talkSPORT, the former Liverpool and Rangers midfielder said: "It's a sad day for Scottish football. For the Old Firm that we talk about being our leadership teams and [what] they represent, it's an embarrassment for our game.
"And as a national team we're trying to improve and we're trying to get better. But these two clubs have let us down as a nation and they have to have a look at themselves today.
"Both football clubs have to look at themselves because they are the standard-bearers for us as football clubs and they have, both [sets of] supporters have let themselves down.
"It's an embarrassment for Scottish football.
"This should not be happening. In this day and age this should not be happening and we have to get control of it quickly because if it doesn't it'll keep escalating and escalating and there'll be big, big problems."
