Silva is still upset about the relationship he had with Emery when the two were at Paris Saint-Germain.
The Spaniard failed to get PSG beyond the last 16 in the Champions League, and Silva admits he was annoyed by Emery's leadership.
"We didn't often agree with each other," Silva told France Football.
"He was the "commander", well, he was paid for that, so I respected his authority, but in the first leg against Real Madrid, he left me on the bench because he needed a left-footed central defender.
"That was his excuse. This is the first time I've spoken about that, but at the time, it was hard to digest.
"He left [Angel] Di Maria on the bench too. We lost 3-1. In the second leg, he no longer needed a left-footed central defender.
"He put me in the starting line-up! It's the kind of thing a player doesn't understand. And this is just one example among many with Emery."
Emery spent a season-and-a-half at Arsenal before being replaced in December last year.