Bundy owed more than $1 million in fees and penalties for grazing his cattle on federal Bureau of Land Management property for decades, and officials tried unsuccessfully to remove his cows, prompting the standoff. The government eventually backed down, though later arrested various people involved.
They were going to remove the cows alright. They were taking them away, not putting them back on Bundy's land.
IIRC, payment had been tendered for the grazing fees, but was refused.