Usage patterns
〈物〉の不足分を補うto make up for the shortfall (in something)
We made extra sales to make up for this month's revenue shortfall.
不足分を支払うto pay the outstanding amount
It was arranged that the outstanding fee would be paid later.
不足分が生じるfor a shortfall to arise
A shortfall arose due to a mistake in inventory management.
不足分を請求するto bill/claim for the outstanding amount
The company billed the client for the outstanding amount.