"What did you say?"
The bI- prefix indicates that the subject is "you" and that there is no object.
But here, there is an object -- the question word "what" is asking about the object of the verb and is grammatically an object.
So you can't use bI- but have to use Da- (when speaking to one person) or bo- (when speaking to several people), which are the prefixes for "subject = you, object = him/her/it/them".
Only in the fixed expressions nuqneH? and nuqjatlh?.
You couldn't say *nuqbom? for "what did you sing?" or *nuqje'? for "what did you buy?", for example.
Also, nuqneH? is not fully interchangeable with nuq DaneH? -- it's an interjection, a reaction to somebody coming up to you, but you wouldn't use it to ask what someone will want in the future, or what they wanted at a specific point in the past. Similarly with nuqjatlh?.
We agree. The only way I can think to complain to staff is to submit a bug report. https://support.duolingo.com/hc/en-us/articles/204728264-How-do-I-report-a-bug-
That is indeed wrong for Klingon and is a "feature" of Duolingo which works well for pretty much all other languages but not for Klingon.
It's point 1c on our list of known issues: https://forum.duolingo.com/comment/26778885
Developers know about this but I'm not sure how far up on their list of issues it is to make a special case for Klingon here.