A kanji might have several readings, but most vocab don’t. Actually, when the same “vocab” has 2 readings, it is followed by a difference in nuance from each.
The readings WK offers is based on what they see as the most common ones. Then, they’ll give the less used ones through vocab. This way, they avoid throwing to you too much info at the same time.
For the Kanji reviews, if you actually try to type a different reading that you encountered on vocab, WK will tell you that they want another reading. They won’t consider wrong because it is not, but they want you to be able to recall the most common ones too. For vocab, there’s no escape. You only have one way of reading them. If you’re mixing the new readings, it just means that you should spend more time on the lessons. A lot of people tend to speed up the lessons, but taking your time is definitely very important. @rfindley is one important member of our community. He finished WK with only around 50 mistakes total. His #1 advice? More time on lessons.
Are you talking about the pitch accent? You can install a script that solves this: