You are leaving out a key point which blows any trust Harry may have had when Carlos and company confronted him on the way back from the Raith estate. Earlier on the beach when Harry had had his run with Thomas in the opening chapter of Peace Talks, Carlos shows up and secretly puts a tracking device on Harry. This says that Harry was a target for some reason even before Thomas went off the rails ...
This isn't really relevant to the question of Carlos and where his trust really lies.
He and Harry agreed to a plan where Carlos was to suck up to the Merlin-loyalist mainstream, lean in on the letter-of-the-law enforcement, and generally work his way up the "traditional" ladder of trust inside the White Council... all the while keeping his ears and eyes open for discrepancies and oddities that might reveal "Black Council" agents.
Now, we can't tell: is he still doing that?
Carlos is acting that way... years later. Without ever touching base & confirming with Harry that he's still sticking to that plan. And similarly, he's acting like his trust in Harry is slipping, like he thinks Harry is compromised, maybe no longer trustworthy.
But then, according to their original plan, Harry was supposed to act just the opposite, the White Council member getting impatient with WC restrictions, making dubious alliances and even allying with rivals and enemies of the WC. Harry has sure been keeping up
his end of things! So of course, "conservative Carlos"
has to act like he distrusts Harry.
And we -- the readers -- are stuck wondering if Carlos really has turned against Harry, or if he's just playing his role so well he's fooled Harry, too!
... Not sure how many or if any of the Wardens know that Thomas is actually Harry's brother, they do know that they are friends ...
I think the first WC wizard besides Harry himself (and Margaret LaFey) to learn of Thomas' parentage (and being Harry's brother) was when Harry told Ebenezer near the end of PT.
... Also Carlos must know Harry well enough by now that approaching him in the manner they did would only backfire..
Indeed; I'd argue that this is decent evidence that Carlos is still on Harry's side: Carlos
staged that little melodrama -- showdown on the dark road -- to demonstrate his own "I'm with the Merlin" credentials, face-down the "problem" Harry Dresden,
and to let Harry in turn demonstrate his "I'm a loose cannon, with dubious alliances and possibly under the influence of Lara Raith" credentials.
By this analysis, Carlos was sending a message to Harry: "look how I set up a confrontation where you
had to refuse cooperation, full of over-the-top melodrama, let's ham it up for the undoubted post-confrontation debrief and likely observers-in-the-dark."