If there are more items than will fit in the shop window, you should be able to scroll in the shop window using the mouse wheel, or by holding and dragging the scrollbar that should appear on the right-side of the screen in the item purchase window.

One thing that I must ask, though, is whether or not you're sure you were at the correct shop - an apothecary will only add its potions to the shop window if you're within the correct distance from the city (don't ask me how far that is - I don't know; it may be that as long as you're within the zone of influence of a city and not closer to another city that you get it, but I'm not sure), as otherwise you'll only have the generic faction store or the shop for some other city within your empire.