Chris Horner's analysis of stage 17 speculates it might have been a bit of payback from Movistar, as you noted.
But Horner said it was mostly tactical errors by the team directors that cost Roglic any lead at all. Particularly, misusing Sepp Kuss as a bottle fetcher early in the stage, so Kuss ran out of gas on the final few km's when Carapaz attacked. Instead J-V used Hofstede for the end of the race, making it seem like he was a key player, when -- again, this is Horner's analysis -- it would have made better sense to use Hofstede to carry water earlier in the race and conserve Kuss for the end.
And maybe the team directors figured Carapaz wasn't in the running for any time bonuses so they weren't going to help or hinder him.