I can't say for sure but it could be. I tried a spray sealant once (Games Workshop) and my custom had the same issue, the paint cracked when I started rehairing the pony. I wasn't sure if it really was the sealant that caused it, but I quickly switched back to my trusted brush-on polyurethane sealant - polyurethane is plastic and it behaves much the same as acrylic paints, it remains flexible. But every now and then I still have the crackling issue, usually it's with pale colours (with lots of white mixed in) and several layers of paint... so it could be the paint too.
If you prefer a spray sealant, it might be best to stick to the brands recommended here. I believe Testors Dullcote is one of the most popular ones?