Translation:We go to that department store, in which there are fresh apples.
"in which there is fresh apple" -- in English, apple has to be used as a countable noun here, so: "in which there is a fresh apple" or "in which there are fresh apples". Probably the latter?
"in which there are fresh apples" should be the English translation of the second subsentence. You are right about the Hungarian translation: Unless you are talking about a specific bunch of apples (Azok az almák...), you have to think of 'alma' and other food items as being uncountable nouns.
Is it an error in Hungarian to put the "van" at the end of this sentence ?
That's correct as well. It changes the emphasis a bit, but the difference is subtle.