"We were missing players but we have a big enough squad that we should be able to deal with that and play our game," Boyata said.
"We don't want to talk about the missing players - we're only talking about the players who played today.
"It was a hard game and everyone is really down because we wanted to leave here with a win."
City were crowned Premier League champions in May, finishing seven points clear of fourth-placed Arsenal.
The title-chasing clubs have all strengthened this summer however and Boyata believes the competition will be closer this season.
"We all know this season is going to be very difficult," Boyata said.
"Teams like Arsenal have done as much as they can in the transfer market to get as close as they can.
"They have bought some good players and it shows. Arsenal, United, Chelsea - they can all challenge."
Boyata was handed a rare start at Wembley. The Belgian joined City as a teenager in July 2009 but he has struggled to establish himself in the first-team.
"I've been here for a long time and I've been doing the same thing every day," the 23-year-old said.
"Hopefully this year can be my year - I'll keep on working and do the best I can to be there and I will try to play as many games as I can.
Boyata added: "The experience of playing today was good but the main feeling is disappointment because obviously we wanted to leave here with a win."
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