According to The Cut Scene, the bonuses were set up to reward the select employees (five of which are supposedly Midway executives) should they manage to sell the Wheelman and Mortal Kombat franchises. The feds and creditors took issue with these goals -- when the "incentive plan" was submitted, Wheelman had already been sold to Ubisoft. The incensed parties also took issue with attaching incentives to the sale of Mortal Kombat -- a duty mandated by Midway's "obligations under the Bankruptcy Code."
There are other troublesome points in the plan, such as the fairly high amount of cash it would dispense -- cash that the owed creditors would like to see in their own coffers. Midway will reportedly file an updated (and likely less lucrative) version of the "incentive plan" before its public bankruptcy hearing tomorrow morning.
Update: The revised "key incentive plan" was submitted by Midway last night and alters the previous plan in a few key ways. Midway CEO Matt Booty has been subtracted from the equation, leaving four out of 28 potential employees receiving bonuses, and of those 28, the bonus will be based on the amount of money various properties are sold at. The sale of the Wheelman property will no longer be considered as part of the bonus requirements and the Mortal Kombat franchise will only count if "all of its assets" are sold along with it. To read more about what has changed, check out The Cut Scene.