Just go through a few phrases on https://forvo.com/guides/useful_phrases_in_czech/everyday_phrases/ to get the feeling how the intonation is rising at the end of a question. The recording here is OK too.
The intonation is wrong in many questions, you have to get used to that.
The intonation is not necessary for anything related to marking. How exactly is it supposed to cause your wrong mark?
In particalar, please be aware that any question marks, exclamation markes etc. are ignored by duolingo.