I think you will probably simply have to accept your deposit back.
Tucked away, and very difficult to find on the TC website is the section

http://www.thomascook.com/site-terms-conditions/

And it has the wonderful getout phrase:-
"Where a price is obviously incorrect due to a system error, we shall not be bound by such price"

TC have been having some terrible problems with their computer systems and website recently.
Sadly it appears you will suffer disappointment as a result.
Try phoning them on a line which isin't going to cost you, and pay them, to keep you waiting.
Politely explain, and hope for the best.
Then....
Maybe you can try kicking up a big fuss, try their Facebook page to get publicity.
Maybe then they will offer something in compensation.
But I wouldn't hold your breath....

Well the first thing I would do is double check all the figures and calculations on the invoice. If they all add up correct then I would go back to TC and tell them so. You don't say where you are going but £600 for the hotel and £300 for the flight sound OK to me if within Europe. It is possible that your invoice is correct whilst something is not registering on their system. Remember computers often do not get things right. If this is the holiday you want then a little time checking might get the result you wish

fwh