The subject and verb are usually swapped in questions, with the subject coming after the verb (though it is possible to leave the subject first as well). Also, in many cases, the subject can be omitted completely, as it's understood by the context.
Take a look at this article. It does a good job describing the typical word order for questions: https://www.thoughtco.com/asking-questions-spanish-3079427
Agreed! As a non-native English speaker, it's extremely frustrating to get errors for misspelling/getting grammar wrong in English when trying to learn ANOTHER language... (Also. We don't even have/use "mr"/"ms"/"mrs" etc in Swedish :'(. ). I forget to use "sir" every single time this question pops up.
Depending on the tone used, mister isn't rude at all. Switching the order around also makes a difference. We would most definitely say "Mr. Smith, do you have two books?" And not "Sir Smith..." In some circumstances the use of the word mister has been corrupted, and can sound smart-alecky, but for the exercise it should be accepted.