The Hornets were put to the sword by Pep Guardiola's free-scoring City side, with Sergio Aguero helping himself to a hat-trick and Gabriel Jesus, Nicolas Otamendi and Raheem Sterling also getting on the scoresheet.
However, despite the one-sided nature of the final result, Silva believes that some big moments in the match went against his side - most notably for two of Man City's goals.
"I think the first goal was offside, the second goal we made a big mistake and maybe the third goal is offside too; this is the truth," he told reporters.
"We had one clear penalty. I'm sure it wouldn't change the result, but would give more confidence in this moment. In the similar moments, they decide one moment for one side and not the same for the other side."
Watford have now conceded 11 goals without reply in their last two home games against City.