Maybe leave a spot in the application for "if you would like to share your pronouns, do so here" then it's more of a "hey if you think it's something that we might get wrong, let us know in advance" and people who get offended can just ignore it and move on. I'm wondering if you asking "what are your pronouns" made them think "I'm obviously a (man/woman) are you saying I look like I might be the other gender?"