Japanese confusing sentences

Ok i am writing this because i am living in japan for the time being so this one is dedicated to all who got confused when they go snack restaurants or coffee shops. now when you enter to a place that would provide serving for you, first thing they will great you with the word (irashaimase)which means welcome, then you head to the counter and the useful thing is that in case of food you will find a illustration of varieties of food you can pickup just by pointing your finger at the targeted food, now here comes the confusing part, you might hear (ten nai de o meshiagarimasuka?) and they say it very fast so this means would like to eat in? I have encountered the same question me and i just said yes, putting in mind that these are unnecessary words just for the complement, but some times clerks to got confused... why?? Here is why,Imagine this conversation between me an the clerk clerk ; irashaimase me ;........ clerk; ten nai de o meshiagarimasuka?((eat in?) ) me ; hai (yes) me ; cafe mocha (onegaishimasu) please clerk ; hai ( kashkomarimashita) i understood me ; take out (onegaishimasu) please clerk; ????? confused me; nothing just had my coffee and walked away.!!!