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 I am a little bit confused by the chest and equipment UI.

 Believe it or not, it used to be a lot worse. Can you elaborate on what exactly confused you about it?

I think it was mainly the part where when you press 'E' at a chest, you get into one UI window. And then, after that, when you press  (I think) 'Esc', you do not exit that UI window, but you enter another UI window, after which you can press 'Esc' again to exit.

I do not know what a better alternative would be. From what I know of GameMaker, one of its weaknesses is likely UI elements. But I have no knowledge of GMS and what features it offers.

I dislike that enemies can be effectively invisible when behind trees. The lock-on helps, though. Have you considered mitigating this somehow, like maybe using a shader to show an outline when an enemy is behind a tree? Or, if enemies are meant to be able to hide, only do it for enemies that the player has "seen"/"discovered"?

I'm planning on having trees vanish when a dangerous creature is hidden beyond them in the future. It's on the to do list.

I wonder whether that would work if you want enemies to be hidden, but I imagine you have thought about those parts since it is on your TODO-list.

I cannot open the chest with "E" if I am standing diagonally from it.

Hmmm, if it's awkward feeling, I can fix that.

I think it's not necessary if a pop-up is added when you can interact with an object using 'E', but if you do not add that or a different method, then I think it would be more ergonomic for players. 

I can discover hidden enemies by clicking "X" repeatedly with the cursor over trees.

How much did that happen? Were there ever enemies who seemed stuck in the trees?

I can only recall of one instance, I think it is when  you are introduced the first time to shooting enemies. Like, a shooting enemy is standing in one place, and then another enemy attacks from behind when you get too close to the shooting enemy. I do not think that enemy was stuck, more hiding. In general, the enemies seemed like they had really good pathfinding.

While the test crossbow is obvious, is there any way to survive the first castle room if you do not pick it up and equip it? Though this may be good, to ensure that the player does know how to pick up and equip items. I just wonder if it may be a source of frustration. I did pick it up and equip it on the first time, though, just speculation on my part. 

Technically it's possible to get through that room without the crossbow, but there's no way for you to know it, because it uses the completely unexplained magic system. The intent was to force the player to both use the crossbow, and probably use kukui juice (antidote) to survive.

I think you could use some playtesting on that. While I would guess that just about no one would forget the crossbow, some may forget to equip it or choose not to, and I would hope that the player would die quickly, such that the player does not have to endure a slow and impossible-to-win-or-escape fight to the death. However, I really like the aspect of ensuring that the player knows how to equip and use items, since it is a core mechanic.

In general, I had fun. I do think my (over-)cautious approach of running the game in a virtual machine and thus the game being rather slower than normal hindered my fun. I think I might have had great fun playing the game if running the game outside of a virtual machine.