They signed him across from South America and nurtured him through their amateur team, promoted him to stagiare deals (which they almost never do) and gave him his pro deal. They were loyal and rode for him even though it was announced before that Giro that he had already signed with Ineos - before Acquadro had even given them a chance to open renewal negotiations with him - and then when they wanted him to co-lead the Vuelta for them, he rode an unsanctioned crit race they'd asked him not to, got hurt and couldn't do the race. I might have thought that plunking Ineos with the bean ball at La Covatilla might have been enough, but you know, you can see why they'd be pissed. Sure, he won them a Giro, but they had Mikel Landa take a back seat and play loyal domestique for him, and given the issues with the triumvirate you can bet that having had to sit in line and play helper for Carapaz in the one race he was going to as sole leader might have played a role in their issues with Landa's contract negotiation too.
So yes, Carapaz won them a Giro, but you can see why they'd see Acquadro as a scumbag a-hole who screwed them over, and Richie as an ungrateful turncoat.
I would say that Movistar could have negotiated an extension at any point after the 2018 Giro. No point in being upset of they have dithered for too long.