Yes, this is right. If you earned 25k in November and December, that's 12.5k a month. The tax system works on you therefore having a 'virtual' income of 150k, and you would have been taxed on those two months accordingly. I too had to question this when we moved from the UK, as the system there would be 'oh, you've only earned 25k, in that case your tax is buttons'.
There'll some tables for Geneva somewhere, search on 'impot a la source canton Geneve' (sorry, can't do accents on this keyboard) and they should appear; then you can check you've paid the correct rate for your family circumstances and salary.
My experience in Vaud is that tax at source is slighter higher than that calculated via a tax return, presumably to stop the dodgy foreign types leaving owing tax; we had an extremely straightforward tax situation (PAYE, no investments, no property) and always got a refund of some thousands each year.