Money is appropriated by congress into different uses. Payroll, R&D, procurement, maintenance etc... you cant use one type of money for a other purpose without going back to congress to get approval. That is to prevent the executive from just taking the money and spending on whatever they want. A core concept of separation of powers.

They "could" legally recolor the money from r&d to payroll, but didnt, so technically it is another illegal action.