The Argentina international was called from the bench as the Citizens beat the Cherries 2-1 at the Vitality Stadium last month.
In addition, Aguero did not play in the Albiceleste's World Cup qualifying draws against Uruguay and Venezuela last week.
Guardiola told Sky Sports News: "[Aguero] is okay. It is because he has two stupid managers that he hasn't been on the field! That is the only reason.
"There are no doubts about the quality of Sergio, but we have to handle a squad of 20 or 21 players. We have to be honest and treat each one the same. It's not that when Sergio plays I am happy with him and when he doesn't play I am not happy with him.
"I'm not a child any more. I am a father with three kids. I just try to be fair with what I believe and what I think. Everybody has reasons and arguments to say 'I deserve to play' - and that's true, but the other ones do too. It is what it is."
Up next for City is a home game with Liverpool on Saturday lunchtime, a fixture in which Aguero has scored in the last five occasions.