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This happened because Trump's administration essentially copy and pasted Heritage Foundation materials rather than carefully think through a realistic budget.
If you spend full budget for the first half of the fiscal year, but a final budget gets passed later that cuts your budget in half- you get no remaining money for the year, and then end up firing everyone, instead of half. This is why the federal agencies have the policy of immediately acting on the lowest proposed budget, instead of waiting to see what happens.