It is possible to have too many links in a chain, in which case you would simply remove one or more. It sound more like this is a case of incorrect adjustment of deraillures. Without more details, it is hard to know exactly what to tell you to change. My first thought is to just take it back to the shop and politely ask them to fix it.
I think that in certain gears, it is not abnormal for a road bike chain to hit the chain stay. This won't happen on a smooth surface, though, but on bumps.
There are several chain stay protectors on the market (stickers, neoprene 'guards'), which can be easily put on, especially if you have straight chain stays. Curved ones are a little bit more complicated.