There are Korok Puzzles with 3 fruit trees in a row, usually apples. Two of them will have only one apple each, and the third one will have multiple apples. There are also puzzles with Durian trees or even cacti and Voltfruit - the setup and solution are always the same tho:

In order to solve the puzzle, you have to remove the fruit that "doesn't match" so that all 3 trees/cacti look the same - and not just "remove all but one apple", but remove ONLY the ones that the other two trees don't have, so that they look abolutely 100% identical afterwards - exact same tree branch, exact same amount of apples.

Just removing ALL fruit doesn't work, even tho the trees will "look identical" afterwards. This can even make matters worse (more about that later).

These puzzles are sadly very easy to mess up: pick or shoot down the wrong fruit accidentally, and you won't be able to solve the puzzle for a while. Sometimes the environment is to blame, when a goat rams into the tree trunk and makes fruit fall down, an Octorok shoots off one of the fruit, or a lightning strike destroys an entire tree. The easiest "fix" for this is to just reload an earlier save file from before the mess-up happened, but depending on how long you have played since then, this solution might no longer be possible, and then you're in for a very long waiting game.

"Random Revival"

Trees respawn instantly every time the zone is reloaded, so if you just save & reload on the spot, the trees will be back again immediatly. The same does NOT apply to the fruit on the trees tho.

Most consumables (fruit included) have a 1% chance to respawn for every minute of IRL active playtime that has passed. Time spent in menus, loading screens, cutscenes etc. does not count for this, and the same goes for when the software is suspended, so you can not just put the console into sleep mode for a couple of hours - you have to actually play the game in the meantime.

Additionally, this respawn mechanic only applies for things that are not on the same map grid as Link, so you have to stay FAR away from the apple in question in order for it to eventually grow back. And not just "out of sight" far away, but rather "different region altogether" far away, as the individual map segments are super large.

^(just for comparison)^

What you should NOT do:

The most commonly suggested "fixes" for this situation are: cut the trees down, wait for a Blood Moon, and skip days at a campfire or inn. None of these help. On the contrary, even.

• Cutting the trees down automatically removes the fruit from the other two trees as well, so in addition to the initial missing apple you now have to ALSO wait for two more apples on the other trees to respawn in order to solve the puzzle.

• Blood Moons have nothing to do with fruit OR trees, so this won't fix the puzzle either. The only things the Blood Moon respawns are weapons/bows/shields in the overworld, and previously slain enemies. And apples are sadly neither weapons nor monsters.

• Skipping time at a campfire (or an inn, or a free bed, etc.) always involves the mini cutscene where the screen goes dark and the cute little nighttime jingle is playing, so you effectively waste a couple of seconds every time you do this. And if you then interact with the campfire/inn/whatever immediatly again, the "timer" might not have advanced at all. It's an easy way to turn a 3-4 hour waiting period into a seventeen hour fiasco.

What you should do instead:

Mark the puzzle on your in-game map and forget about it for now. It will regrow eventually, but since there is a hefty amount of RNG involved, there is just no way of telling HOW long it will take in the end: might be 15 minutes, might be 15 days, or anything inbetween. Sadly there is no (known) way to speed this up, just lots of disproven rumors that will make you waste your time.

Be patient and don't bother checking the puzzle every half hour or something like that, as this might delay the respawn further (as you're on the same map segment again).

A watched pot never boils. Just do something else for a while.

In-depth explanations about the various respawn mechanisms can be found here: https://zeldamods.org/wiki/Object_respawning

All of this data is based on the actual game code, so there was no trial and error involved.