They would have had a contract to deliver a game by X date for X amount, there may have been incentive bonuses, e.g. you get X more if it is metacritic 8.0+ or you deliver on time.
I'd say a lot of the problem with this game probably started with that contract, SEGA must have really left a lot of loopholes. For example I'd stick in a clause stating that no part of the game development should be outsourced. It's just a line, easy to do, but think of the difference that could have made to the final product.
At the end of the day SEGA got the bare minimum of what they paid for in the most cost effective way for Gearbox. I'm sure SEGA learned some lessons on contract writing after that.