Before kickoff, Guardiola told Sky Sports "we don't have any more" when asked about the decision, explaining that the club's U23s were involved in a game on Friday night.
But pundit Neville was unimpressed with that explanation, arguing a young player should have been given the seventh spot.
"I think it's a joke, I absolutely think it's a joke" Neville told Sky Sports.
"If you're a youth team manager at Manchester City, ring him up and ask which kid deserves that boost. Who has been playing well this season and who has worked hard?
"Forget the second team. Even if they played yesterday, bring one and put them on the bench. Bring a kid to travel with the team, help the kit man and put him on the bench to have the experience of being in a Premier League game. Give someone a boost at the club.
"If you're the Academy or reserve team manager at Manchester City you must think 'I'm wasting my time'. Forget the fact they've spent however much money, six players on the bench… to me it's like a protest.
"I'm not sure why he's peddling this theme. He's an absolutely incredible manager and the work he has done with this team is unbelievable and the team performance is absolutely outstanding.
"Things like that let you down. He doesn't need to do things like that."