Stations essentially on the same site but on split levels (such as London St Pancras, Liverpool Lime Street, Glasgow Central etc) are counted as one station.
Stations are counted as seperate if one has to walk or catch another form of transport to travel between them. As a general rule of thumb, stations are considered to be seperate from each other if they are identified with different names in timetables; Stratford and Stratford International or West Hampstead and West Hampstead Thameslink for example.