On Hale's page, Relationships, Bernard was tortured by Hale but this is really unture. Hale is actually dead and that is Dolores posing as Hale during those scenes. I am not sure when Hale was killed in Season 2 but some scenes during Season 2 is Dolores in Hale's host body. We just didn't know until the finale.
Hale was killed before Strand's extraction team reached the beach, so anything that occurs after that with Hale should be Dolores in the Hale-lookalike host. So every interaction that Bernard has with Hale from when the extraction team reach the Mesa is with Dolores, which includes Hale meeting the extraction team, discovering the Bernard hosts, and Hale's torture of Bernard. She obviously keeps the secret until Bernard remembers what he did, throwing the interaction with him when he reaches the Mesa with Strand in a different light.