Carlos Vinicius jumped from the bench to score the only goal of the game in the second-half.
Silva later said: "Difficult one and to be to be honest, we expected that," Marco admitted. "We expected that 5-3-2 always behind the ball. This afternoon they did it different with 5-4-1.
"Not something that we face every single week at this level. But we had to get used to that and show respect.
"I respect all the teams, all the strategies as well. Huge respect for Luton, I repeat again, what they did last season was unbelievable.
"They deserve the credit, they are fighting for something really important to that football club.
"First-half, we lacked something dynamic to be honest to create chances. Second-half, some improvements, more dynamic and the two changes made a huge impact in the game."
Silva was particularly pleased with Alex Iwobi and Timonthy Castagne on the day.
He added: "Nice to see Timothy impress out of his natural position, even if he can play left or right. He can play both sides so well and he's a great addition for us, definitely.
"Nice to see Alex come in and get his first minutes. They are going to improve for sure, the way we play is going to make them better players for sure. We're really happy to have them."