O'Neill insists naming only six substitutes for their FA Cup third-round draw at Bolton was not meant as a message to owner Ellis Short.
"It was not a point whatsoever, it is the way things fell," said the Northern Irishman, whose selection problems mounted with the loss of defenders Danny Rose and Carlos Cuellar to injury.
"I think I get on reasonably okay with the owner. He is well aware so I think he wants to do something about it.
"We had a couple of injuries and illnesses, we don't have the biggest squad and we were really stretched but we've lost a couple more.
"We are trying to do something about it if we can, we need to.
"We couldn't change it much today because we couldn't fill the bench but we treat the competition with its proper merit.
"I don't care how many games we play - I'm told it's five in 15 days - we wanted to be in the competition and do well in it.
"We had 5,000 people spend a lot of hard-earned money to come down and support us and they deserved better than we were serving up in the first half."