I bought a pair of wheels that were advertised as mk2 wheels however the front wheel won't fit as the bearings have a smaller inner the hubs look the same can I just fit a set of mk3 bearings to the wheel?

Measure the bearing size. You will probably find that you have bought a set of Mk1 wheels. These use a 15mm spindle as opposed to a 17mm for the Mk2 upwards. I don't think that you can get a standard bearing that will fit but I might be wrong..........

If the above is correct and you bought via eBay you are entirely within your rights to ask for a refund as they have been wrongly described.

On the other hand you may not have the original front end on your Mk3?

If I measure the bearing size what should they be? The hubs look identical