Having played through it the twice, I decided to write down the bugs and post what I've encountered here. Be warned, as I have almost thoroughly played through the game to search for them, it is long. I've listed them chronologically for each category.
Excess keys:
-Hyrule Castle (key under a pot in Dungeon room with Zelda captive and a Ball & Chain Trooper)
-Eastern Palace room before boss (2 keys under pots at this point are moot to have)
-Thieves' Hideout (removing a couple from the beginning rooms that are under pots couldn't hurt. There's 7 total before the Big Key Lock. :/)
-Ice Palace (under the left pot that's just in front of the block that leads to the boss floor is another key that is moot to have)
-Misery Mire (like 12-13 keys total in the dungeon, please one that is dropped by one of the eyes that die after defeating Virteous, the boss); gamebreaking, see last section
Keys are lined up together but some disappear after only picking up one of them:
-Hyrule Castle main chamber (3 keys aligned vertically, top two keys disappear)
-Eastern Palace entrance (3 keys aligned horizontally, middle and right keys disappear)
-Desert Palace entrance (3 keys aligned horizontally, middle/right keys disappear)
-Thieves' Hideout (3 keys in rectangular figure, top-left and bottom-right keys disappear)
-Misery Mire entrance (4 keys lined up horizontally, three leftmost ones disappear)
-Turtle Rock entrance (3 keys aligned horizontally, middle/right keys disappear)
Enemies still in the game:
-Kakariko Village (2 Mice in the bombable shed in SW portion of the village)
-South of Link's House (the Rabbit that pops out of the grass; disappears after entering the Dark World like usual)
-Entire Zora's Fall area (heard this place is "special" so probably nothing can be done about it)
-Tower of Hera 5F (Blue Spider and a bumper)
-Entrance to Death Mountain (After entering Dark World, there's a blue Knight at the north part of the screen there are 3 Crows that are on the series of trees at the southern part of the screen)
-Dark World (2 Bull Knights & a Medusa [it's stuck] one screen south and east from Pyramid of Power
-Dark World (2 Bull Knights & a Medusa one screen east of the above area)
-Dark World (2 Bull Knights & a Medusa at the Bomb Shop area)
-Dark World (1 Medusa one screen west of Bomb Shop)
-Village of Outcasts (Ghini in NE section of area)
-Thieves' Hideout (1 Gel in the cell room with the fake maiden)
-Turtle Rock (1 room west of room with Big Key Lock; under bottom-right pot is star thing that transforms you into bunny)
Glitchy chickens that appear in pots
-Eastern Palace (dark room en route to Big Key)
-Dark World cave (right cavern system that connects the lower-right portion of Death Mountain to upper-right portion)
Keys That CANNOT Be Picked Up:
-Tower of Hera 2F entrance (first floor, NW portion of room)
-Ice Palace (a key just in front of the locked door in the second room); gamebreaking, see last section
-Turtle Rock (key in Chain Chomp room)
-Turtle Rock(2) (key in eastern-most room on B1 which is the route to the Big Key)
-Ganon's Tower (visible key in center of the room that is before the big room with big Moldorm aka Tower of Hera boss)
Miscellaneous:
-As there more heart pieces than in the original game, you can technically get more than 20 hearts, however getting a heart container(be it by Heart Piece or boss) after 20 hearts will do
nothing, so no harm, no foul.
-Tower of Hera 6F (boss room): New pots have nothing under them.
-Dark World: Unobtainable heart piece 2 screens east of Swamp Palace.
-Thieves' Hideout: Hard to describe, but it's in the first rooms of the dungeon. Without that certain trigger that causes Link to jump from a higher platform to a lower one, he just walks in mid-air.
-Ice Palace: If you enter the most northern room at B3, you'll need to use the Magic Mirror because you'll be stuck since the falling tiles that send you downward have been removed.
-Misery Mire: A few rooms into the dungeon, the same thing as in Thieves' Hideout happens.
-Ganon's Tower: In the center room on Floor B1 (where it intersects the paths that have the Compass and the Map) where it is one room south of the Big Chest, there is a transporter. If you step on it, you'll be transported to an icy-decorated, empty room with no exits. You'll have to use the Magic Mirror to escape.
Ganon's Tower(2): In the room with the icy floor and Armos Knights, there's only two. After they awaken, they just..hop to their designated positions and stay in place until you kill one of them. Then the remaining one turns red and moves normally.
Game. Breaking. Glitches.
-Swamp Palace: Arrghus IS NOT IN THE BOSS ROOM. No boss fight, no Crystal, no Ganon's Tower. I think this has to do with wiping out the other enemies in the room set on B1 that has the boss room; I don't know for certain.
-Skull Woods: The movable statue has been removed from the room that has a button required to be held down to gain access to the room with the Big Key. This causes sequence breaking until the
Cane of Someria can be obtained from the 6th dungeon Misery Mire.
-Ice Palace: The only key before the first locked door cannot be picked up. Without beating the Ice Palace, you cannot get the Crystal, ergo, no Ganon's Tower.
-Ice Palace(2): After entering the room with the Big Key Lock, if you drop in the holes in any direction other than the blue blocks right beside each hole, you won't fall into the fairy room and instead you'll be stuck. No buttons will respond except the directional pad (Link himself can't move outta the stuck spot, though). The game will have to be restarted.
-Misery Mire: After defeating Virteous, one of the 4 eyes that are left that are automatically killed will leave behind a key. IF YOU GRAB THIS KEY, THE GAME HAS TO BE RESTARTED. The reason why is if you get the key, the Crystal CANNOT BE GOTTEN. I repeat: the Crystal CANNOT BE GOTTEN if you grab the key. If you otherwise ignore the key, though, you can get the Crystal.
There might've been a couple things I missed, like a garbled fairy in one of the caves, but I can't remember for sure. This concludes all the bugs I found in this beta.