The thing about Carlos is that he's very much Schrödinger's Ally to Dresden -- we don't get to see inside his head, we don't know what's going on there.
I go back to the groundwork laid in White Knight, between Harry and Carlos.
Carlos challenges Harry as to Harry's motivations & alliances, there in the Raith Deeps, before the fighting starts.
Later in the hospital, they have something of a reconciliation... and they set their own private alliance: not White Council, not Grey Council, just Harry and Carlos as trusted allies working to uncover the corruption within the WC. Working the problem from both ends, towards where it meets.
Thereafter, they must act as if they are growing apart. Carlos, in his role of "White Council Warden, trusted and trusting and reliable" cannot be friendly with someone like Harry, in his role of "rogue wizard, delving ever deeper into darker & darker paths & alliances."
. . .
All of the hostility & negative stuff might 100% be Carlos playing his role.
Or, it might be Carlos becoming more suspicious and distrustful of Harry.
We don't really have any way to be certain, because we don't have a view inside the box.