On the flip side you don't pay the fee and wages for a player at his age with only 12 months left on their contract unless you're sure they're going to improve your starting XI. If he's just there to be a squad player then why bother? So it wouldn't be off for someone to say not getting chosen to start for both Madrid games is a bit of a red flag for someone that was expected to be a difference maker.
But the context we are in, and the exact context of the game(s) in question were not known when the player was bought and the fee paid. There's only so much foresight a manager can have, and this season has thrown foresight, and expectations, right out of the window.
In any case that was just one example that I gave; another might be that there's nothing wrong with Thiago, in the manager's eyes, but rather that another player is just not currently meshing with him; if the manager decides that that other player is essential for that game then maybe Thiago has to start on the bench while a player who will combine well gets the start. There's a lot more to selection then just picking the best players like we used to in the school playground..
And it's not like he's been shoved into the reserves. He's a key part of the match squad, and got significant minutes in both games.
Another aspect people are overlooking is that the five subs provision can affect the manager's selection, too; knowing he has the luxury of bringing players on in a strategic way, rather than just a reactive one.