"Is there pork in that store?"
I define this case as a Duolingo sentence with no context saying "is there pork in that store?" Of course we want to be polite when we need to be polite, but there's nothing in the English to indicate the level of politeness. You could be talking to a stranger or your best friend. That's what I meant by my comment.
そのお店には豚肉がありますか？would be much more natural. は in the middle of the sentence highlighting the meat like that feels very akward. The topic is most naturally expressed in the beginning of a sentence. Although there can be an entire sentence modifying the topic. E.g. 先の話したお店には豚肉がありますか？
You use で to show where an action is happening, while you use に to show where something exists. あります (arimasu) is a verb of existence, so we use に with it instead of で (which you can see is the main answer at the top).
You can also use は with the place to put emphasis on it. It's like saying "is there pork in that shop?"
I just know from getting this exercise that it's what the answer banks will accept at the moment. Maybe it is like the difference between ふろ (bath belonging to me) おふろ (bath belonging to someone else)?
The good news is that the Japanese course will be getting a big update.Often, when a 2.0 tree is released, any 1.0 material that is kept gets an update to the answer banks. :)
That difference you’re stating about furo and ofuro is not a usual usage as far as I know. Many people refer to their own bathroom/bathtub as ofuro. With mise the honorific お is just to be more polite, so I would hope that みせ has been added to the database since you asked your question a year ago. I think it’s more likely that using には with みせ hasn’t been added to the database yet and just needs to be reported.