"IRS rules state that you cannot borrow money from an IRA to make investments and you can't use IRA assets as collateral. When you sell a stock short, you must borrow the shares from your broker to ensure they are on hand when you complete the short sale...This makes a short sale a prohibited transaction for an IRA."

from: Can I Short Sell In My IRA? at Pocketsense

so I'm guessing they would effectively be doing an unwanted distribution if they did in fact borrow your shares in the IRA without telling you. Your probably good..