As @aaron9eee says, it's never too late to enforce rules as written (RAW).
However, you say you haven't talked to your player yet about it. That should be your first step! Your player clearly knows something is wrong, so take them aside out of game and 'fess up: "I recently found out that we've been handling some of the monk features incorrectly. The game balance relies on us using these features the right way so that everyone can have fun. I'm sorry I didn't catch this sooner!"
(Note: I prefer to use "we" when having these kinds of conversations; it avoids making it sound like you're accusing them of cheating or being "stupid" somehow. And it acknowledges that you could have looked up the rules earlier but didn't, so they don't feel alone in this.)
After that, listen to the player. They'll likely have concerns about what this means for their character going forward, especially if they've made level-up choices based on the incorrect rulings. I'd recommend offering the player a free chance to restat/re-spec by the book. This lets them feel like they're involved with fixing the mistaken rulings, rather than just being punished.
If you're not comfortable allowing a respec, still listen to your player's concerns and do your best to find ways to help them adjust to playing by RAW. Remember, and remind them, that you aren't doing this to punish them. You're doing this because you want the game to be fun and that means making sure you're using the system correctly (or at least, making informed choices about when and how to homebrew).
I actually just had this conversation last week with my players after we all switched to a new system and several folks realized they misunderstood how their classes worked. I set limits on the respec - no complete character concept overhauls, but stat bonus adjustments, feats, spells, etc were all fair game. Some of my players are taking me up on it; I think at least one other is choosing not to because they see it as an interesting challenge to play the character as originally built despite not understanding the mechanics. Either way, the most important thing for my group was acknowledging the issue and agreeing on a solution.