Why is the Iron Bank calling in loans on the merchants if their focus is on Iron Throne debt?

To put pressure on the regime, the same way that the IMF, EU central bank, etc. used pressure on Greek banks to pressure the Greek government. 

If merchants can’t get loans, then they can’t generate the commercial activity that the monarchy taxes. This is intended to make the regime see “reason,” and barring that, weaken it so that the Iron Bank’s chosen replacement can more easily triumph.