No it does not mean that banks will or even always have made a loss on tracker mortgages.
A tracker mortgage is linked to another interest rate. In Ireland trackers track (i.e. change with) the ECB interest rate. They were offered by banks as at the time it was a reasonable assumption that the cost for the bank borrowing the money to fund the mortgage would be continue to be close to the ECB rate. The money they make is the difference between the interest rate they pay and the interest rate you pay. The money they borrowed was on a much shorter term so they have to keep reborrowing to finance your mortgage. Unfortunately for the banks, this hasn't remained true and banks have found themselves paying more to borrow money and not able to up the rate of interest they charge you.
So you borrowed 100k @ ECB rate + .95 in 2006, the bank borrowed that money for a month from a bank in Germany for ECB rate + .1. Happy days for bank, bank refinances as it needs to always looking for the lowest interest rate it can get. jump forward a few years. Credit crunch happens, bank is trying to refinance your mortgage, but now it finds that the lowest rate it can obtain is ECB rate + 2.5. Bank is stuck, it has to refinance but it can't recoup the full cost of that from you because of the tracker. Bank loses.