this is probably a hold over from the content overhaul, when some of the readings you learn with the kanji were changed to on’yomi.
so the three vocab are the transitive/intransitive pair 始まる・始める and 始めに, which is a common expression derived from 始める (ren’youkei + に). so you actually only learned two verbs.
The on’yomi reading し on the other hand is used in a lot of jukugo (kanji compound words, like 開始、始発、始末,始業… See how the on’yomi is actually more useful in that regard?
Maybe we should summon @anon20839864 or @CyrusS to weigh in? In any case, when you find bugs, a quick email to hello@wanikani.com usually makes things better.
I tweaked the reading explanation for 始めに to say the reading was learned with 始める instead of the kanji.
As for teaching the on’yomi reading with the kanji, we definitely want to stick with that. It will make it easier for everyone in the long run (especially if we add things in the future).