Arsene Wenger’s side needed extra-time to beat Norwich 2-1, while Pep Guardiola’s men had to win a penalty shootout to see off Wolves.
Both Premier League sides made two substitutions in the additional 30 minutes and now the Canaries will seek clarification from the Football League over the rules, according to The Sun.
Four subs are now allowed in cup ties this season but the rules imply only one can be brought on after the initial 90 minutes.
Carabao Cup Rule 10 states: “Each team is permitted up to seven substitutes of whom not more than three may take part in the match.
“Where any match goes to extra-time each club will be permitted to use an additional sub (in extra-time only).”
The officials – Andy Madley at the Emirates and Kevin Friend at the Etihad – allowed the two subs in extra-time.
Arsenal boss Wenger thinks he complied with the rules and when asked he said: “Yes.”
Norwich manager Daniel Farke added: “I think the rule has changed but it is complicated.”
If the Carabao Cup think there has been a rule break they could expel both clubs but would be far more likely to make them replay their fourth-round ties.
It is not the first time the rebranded competition has made the headlines for the wrong reason this season.
There was an error in the second-round draw and the third-round event was held at 4.15am in the UK.
Arsenal return to Premier League action this weekend against Swansea.
Leaders Manchester City will travel to West Brom on Saturday at 3pm.