Shouldn't this be せい since it's asking for the On'yomi?

WaniKani teaches the kunyomi for 星 when they teach the kanji. Where did you get the impression they were asking for the onyomi?

Sometimes it teaches the kun’yomi first, usually because it’s used much more often. Whichever reading it teaches first is the reading you use on the kanji review, and it will teach せい later in a vocab word it’s used in.

Pink means something is a kanji. WK teaches you one of their readings. It can be onyomi or kunyomi. If you’re level 6, this isn’t the first time it’s happened to you. You learned たま for 玉 and いし for 石 in level 2.

I am confused about the choice which reading is being suggested to learn.

For example, for the kanji stone 石 reading to learn was 石 (kun). But when you look at all the vocab words only one (the obvious one) is using kun reading. All others are using on reading.

In that case, it’s because even though there are more words that use the on reading, the kun reading vocab word is more common than all of them.

石 いし appears at #1931 in this frequency list. Next is 石油 せきゆ (oil/petrol) at #2474, which does use the on reading. 石川 いしかわ appears next at #5178, with the kun reading again for the place/family name. 石原 いしはら and 石井 いしい, two more names come in after that. So you’re past the 6000 most common words in Japanese and いし is dominating the list.

The on reading finally returns with the appearance of 宝石 ほうせき (jewel/gemstone) at #8029.

Funnily, at #8789, we have 流石 さすが (as expected), which is a reading not even taught by WK.