The Hornets lost Costel Pantilimon and Nordin Amrabat on deadline day, despite the latter having started all three of the club's opening Premier League fixtures and being included in their 25-man squad for the rest of the season.
Silva revealed that the decision to loan Amrabat out went against his wishes, hinting that the club's hierarchy were responsible for weakening the squad.
"Now the market is closed, I don't want to talk much about it, but first, I'm clear with you, the last week was not the best for us in the market," he told reporters.
"It's different than what we tried to do, but different things happen. What we planned for last week and achieved is different. You want the best things, and you can't achieve that in the last week.
"That's not the best thing for me or Watford, but that's life. I expected something different, it's true. In some moments the coach can't control everything. Even though we lost one player after August 31, it was not in my plans to lose the player."
Watford will look to continue their unbeaten start to the season when they take on Southampton at St Mary's on Saturday.