We still don't know if all of the hosts in the park actually have free will, or if they're still acting out a narrative that Ford created.
At this point, we think Bernard is acting on his own free will, but there is still a chance that Ford could have written this glitching into Bernard's narrative.
In the season one finale, right before the dinner where Dolores shoots Ford, he tells Bernard, "In order to escape this place, you will need to suffer more."
Ford knows more abut Bernard than anyone else, since he's the one who made him. Ford gave him a backstory and assigned him countless narratives to play out, so Ford probably knew how much this overload of memories would affect him physically.