The west London club arrived back in England at 5am on Thursday morning after their 2-1 win over Atletico Madrid.
Boss Antonio Conte complained about his side having to play on Saturday night instead of Sunday, and Fabregas has repeated similar sentiments.
“We knew it would be a difficult week starting with the trip to Stoke last Saturday and then Madrid,” said Fabregas.
“We practically had only one day to prepare for the City match, while we faced a team who were well prepared.
“They had played two home games and had an extra day rest.
“We are making no excuses. We gave it everything but they are a great team.
“They had won their last two games much in the same manner we did, so congratulations to them.”