When you sell stock short, unless you arrange for a pre-borrow, the actual borrow does not take place, nor are borrowing costs incurred, until the trade settles. Similarly, when you close out the position, the borrow is not returned, and therefore any borrow costs remain, until settlement date. Settlement date is generally 2 business days after the trade date, which can result in fees being charged over a weekend or holiday.
At the moment pre-borrow is available to Portfolio Margin accounts at IBLLC and IBUK.