I have a simple theory as to why Thrawn let the Ghost crew get away, twice. The Ghost crew is amongst the most visible elements of the Rebel Alliance: a Lassat (endangered species), a mandalorian which leaves graffiti everywhere, 2 Jedi (or trainee) wielding lightsabers, etc. They are also, in many cases, acting as the tip of the spear for the rest of the Alliance.Thrawn is not interested in destroying the tip of the spear; he would rather be able to predict where the tip is intending to strike so he can destroy the spear itself.That’s my 2 cents.
I'm not disagreeing that this is his plan .
My point is merely that not everyone in the Empire might see that, and if you have a chip on your shoulder (or are looking to get a promotion by 'backstabbing' a superior officer to get them out of the way), his actions could certainly have the appearance of being sympathetic to the Rebel cause. Enough to report them, anyway - and if the Emperor, his advisors, or the heck even the Moffs are hearing that often enough about him from enough different people...