In class I remember my 老师 said there is a difference between 店 and 馆。 For example: 咖啡店 and 咖啡馆。In this context what is the difference?
I think your comment is right, although in my (admittedly) more colloquial Taiwanese-y Chinese, I would probably call it a 咖啡站 instead of a 咖啡館. However, a 店 is probably a store where you buy supplies related to the product.
Supplement to Tang Ho's answer: Note: Sometimes you can't tell the meaning of a word from a single character consisting that word. So the following explanation is applied to a character:
店：originally mean warehouse in ancient time, now expand to "place sell goods or service", for example: inn, shop, fair.
馆: Divided into two parts: left part is "餐", right part is "官". Guess it originally means an official place to provide meals and rest. Now it could be:
accommodation for guests
live, reside (verb. Classical Chinese)
collection e.g. 馆藏
restaurant e.g. 馆子
店: 1.商店，卖东西的铺子 杂货～|～铺|～员。
馆： 1.供宾客、旅客居住的场所 宾～|旅～。
4.某些服务行业店铺的名称 饭～|茶～|理发～|照相～。 The first translation of 店 sometimes has the same meaning of the last translation of 馆 and the second translation of 店 sometimes has the same translation of the first meaning of 馆。
i don't think there is a a difference. Technically, say 咖啡馆 is more oral, 咖啡店 is more literal.