My comments on this are not necessarily directed at the fact that the finish bubbled, but instead more of a general comment on the bond of the clear coat to the paint...
When I first started building, I used to use primer on the bare wood. The primer seem to be the weak link in the bonding process and on a few baits I had some 'delamination' where the finish and paint separated from the bait, at the primer level.
I stopped using primer and instead began sealing the baits with sanding sealer, then a thin coat of clear (followed by a bit of light wet-sanding) and then I put down a coat of white paint, not primer, as a basecoat. I then paint and finished the bait as per usual.
The wet-sanded clear coat seems to provide a much, much stronger base upon which to build paint layers compared to the somewhat chalky primers that are commercially available.
I have had zero problems with delamination ever since.