The former Shamrock Rovers manager said the conditions in Valletta made things difficult for his side but conceded that they were lacking in the final third.
"It was a difficult game in that the conditions weren't particularly conducive to trying to play. The pitch was difficult, very bumpy, the wind obviously didn't help matters," Sky Sports News quotes him as saying.
"But overall, whilst we never really seemed in any great danger and we controlled large portions of the game, we didn't create enough chances.
"They were very well organised and at times we played into their hands a little bit with our choice of passing. I think at times a little bit of our inexperience in certain areas of the team showed up."
The stalemate means that O'Neill has yet to record his first victory since taking change of the national team, with five draws and three defeats to his name.
"You want to win games, simple as that. We've had eight games, we've had five draws and three defeats. We've had some very difficult games in there," he added.
"Of course it's a concern but at the end of the day the only people who can change that are myself and the players and I'm aware of that."
Northern Ireland's next game is a World Cup qualifier at home to Russia on March 22.