This is a result of the original design. Kbin, up until just before the peak traffic hit, was using boosts as upvotes and favorites/likes were just below the post/thread (where boost sits now). Lemmy does it the way it is now (likes = upvotes) so Ernest changed it to match Lemmy behavior. But just as he changed it, he hadn’t changed the calculation for reputation to match when the server nearly melted down and he has to spend all his time just trying to keep the site alive by himself.
PSA: Upvote is not an upvote like you are used to (like Reddit) - "Boost" is the Reddit Upvote (kbin.social)
Like the title says, if you want to upvote something on KBin, you should use the Boost link, not the upvote button (Why? Don't know...)...