The amount of total fuel on board on landing and the fuel available to run the APU need not be the same.
Type dependant, the APU can only be fed from one or some tanks and the fuel in the others may be usable only to the engines but not to the APU. Also, there are APU installations around that require a minimum fuel level way above the unusable ullage in their respective supply in order to be run, further limiting the operating time in such a situation.
Now, I will not claim to have any knowledge about relevant systems in the type used by Air Transat, so let me just say this one thing: While this occurrence may well have been easily avoided by calling in for fuel or possibly an external air conditioning (of course in the absence of electric storms leading to a stoppage of handling!), the information given on here does not really allow throwing accusations of landing with lower-than-prescribed fuel.