The Blues won 2-1 in Spain thanks to an added time goal from Michy Batshuayi.
It leaves them top of their Champions League group with two victories from two games.
However, Conte quickly turned his attention to this weekend’s crunch showdown with Manchester City.
Pep Guardiola’s side travel to Stamford Bridge on Saturday evening (5.30pm), having had an extra day’s rest.
City beat Shakhtar Donetsk 2-0 at the Etihad last night, without having to leave Manchester.
Chelsea fly back overnight and subsequently have less preparation time for their showdown - leaving Conte far from impressed.
“It’s very difficult when Atletico Madrid score to come back, but despite this we did well to win,” Conte said.
“We played with good personality and we kept our head on the pitch at all times. Against a difficult team like Atletico Madrid this is a good win.
“Now it’s important to rest and recover because we don’t have much time before the game on Saturday against Manchester City.
“Honestly in this case I feel a bit penalised and I think it is important to analyse the situation.
“Tonight we play away and we return to London at about four o’clock tomorrow morning.
“To only have one day to prepare for this game is not right. It’s not right.
“Honestly I’m very surprised to see this big game played on Saturday and not Sunday. But we want to be ready and we need to face this game now.
“Manchester City are a very strong team and they are scoring a lot of goals so we need to get ready for this game. But someone needs to analyse the situation.”
