Not sure if the tiles are related to the ones on the shuttle but they could be.
They're not. Both are ceramic based, but that's as far as it goes. The solid ceramic aircraft tiles are far more durable than the foamed ceramic from the Shuttle.
I have to watch out in areas where I applied a lot of glue as it seems to be affecting the putty. I've noticed a couple of cracks in the putty even after it was dried and sanded down. There could be traces of vapor finding its way out yet.
The small cracks are a result of the residual amounts of solvent in the putty continuing to dry even after it appears nice and solid causing the putty to shrink and then crack. For places where the spot and glaze type putty is more than a .020-.030" thick, this will continue to happen for quite a while. Weeks. Months, in some cases. The only real way to avoid it is to apply in very thin layers (like .010" per layer) and let dry for week or so between layers after sanding.
For this reason, for any areas where I am doing any real shape changes, like you are doing here, I use 2 part epoxy putty, like Miliput or Aves (prefer Aves). These do not dry, but cure. There is no releasing of solvent so no shrinking. They have their own issues, but shrinking and cracking isn't one of them.
Paul