If John Hammond was known for "sparing no expense" all things Jurassic Park, why was Dennis Nedry so underpaid?

Greed and budget overruns explain Nedry's behaviour

The movie contains a good deal less information about Nedry's history and motivations than the book. But both make at least two main things clear.

The first is that Nedry is greedy and unprincipled. He wants even more money than Hammond had already paid him. The second is that he sees the potential success of the project but has no mechanism to extract any more from Hammond. And HAmmond has lost patience with Nedry due to underperformance and his attitude, hence why he won't pay him more.

The book has more detail to flesh out both, interrelated, motivations.

He has already been paid handsomely for the project. Hammond was generous. But the project has overrun, more than once. And Hammond has grown tired of both the delays, the failures and Nedry's demand for more money to fix them. Hammond has set a limit on future payments and set a deadline for completion (he might even think that Nedry is, effectively, blackmailing him because the software is so essential for the whole project. Nedry's character is not especially apologetic or diplomatic about missing his deadlines or blowing his budget, so Hammond's attitude seems understandable. And this means that despite Hammond's normal "sparing no expense" attitude he doesn't like to be gulled by an awkward contractor and has clearly lost patience with Nedry's attitude and capacity to finish the work.

The important thing that triggers Nedry to attempt to steal the embryos is that Hammond has made it clear he will not concede further extensions or budget. So Nedry has no route to "getting his share" or, possibly, getting any more money at all. But Hammond's competitors will pay generously, not for software, but for the embryos. They could not replicate Hammond's work quickly or without vast expense. So they are prepared to pay a great deal for the core material that avoids this expense. And Nedry is both greedy and can't extract more from Hammond, so he is an easy target for subversion.

Nedry's alternative choice would have been to eat his own budget overrun or admit failure and take any penalties. These probably look like a very bad options as both would make him poorer (with admitting failure seriously damaging his reputation as a programming genius).

He sees an easy way to get richer by exploiting his situation but without having the finish the project or work for free.

Nedry is a contractor. As a contractor, you estimate your time and submit a bid for the project based on your estimates. Clearly Nedry underestimated the project, but Hammond was under no obligation to pay him more than the estimate.

To your point, if he truly "spared no expense" he'd pay more than he was billed for to keep Nedry happy. But if someone comes to your house, submits an estimate for installing a new hardwood floor, and then runs over budget due to their own incompetence, are you going to pay that contractor more than you agreed to? I sure wouldn't.

There's a scene where Nedry is really hammering Hammond about being underpaid, to which Hammond replies:

I don't blame people for their mistakes, but I do ask that they pay for them.

This is an allusion to the fact that Nedry underbid the project, and Hammond is making it clear that this is Nedry's problem and not his.