This was part of a recent UI change to make flagging more obvious.
As mentioned by Monica, this is an intentional change to make flagging more discoverable. We can all agree it definitely does that.
This is a work in progress and we are working on some additional changes to improve the layout of comments. These changes will build on the changes we made to make comments responsive and will use our Stacks design library. As you can imagine and as this post proves, changes to comments layout can be controversial, so I'll post more as we rollout additional changes.
Why are the comment upvote and flag options always appearing now?
Some CSS can reverse this change:
.comments-list > .comment:not(:hover) > .comment-actions > :not(.comment-score) {
visibility: hidden;
}