it's been a while since i've read the book, but i do think ingen also recovered genetic material from ground up bone. if you think about it, why would a company in ingen's position limit themselves to dna found preserved in amber? the dna found in the amber was probably the least fragmented, but, once enough high-quality dino dna had been collected, that dna could likely have been used to help reconstruct sequences from other sources. i know there's no mention of these techniques being employed, but they're the most likely, especially considering that dna would be flowing in from multiple sources and, in many cases, a single sample would contain contributions from multiple animals, most likely representing multiple species. the fragments would likely be labeled by source, location, and time period, sequenced, mixed with dna from other sources (such as frog dna) and then aligned using a strategy similar to shotgun sequencing (
http://en.wikipedia.org/wiki/Shotgun_sequencing). that being said, there were probably plenty of opportunities for mosasaur dna to end up in an insect and for that insect to end up trapped in amber. two examples i can think of are a beaching scenario or a carcass washing up on shore.