Most of those glitches are well known if you took the time (like me, yes i have loooots of time)
and read the thread you'd know these glitches.
And the mother one would need a new sprite table as she only has facing frames.
Sorry, I didn't get enough time to look through every single post... TL;DR syndrome got the best of me. :P I'll try to look through and re-post only the ones that haven't been mentioned.
Here's a list of ones I have encountered:
Healing machine in Maple's lab has wrong script when talked to from behind.
Tile in Nile City has wrong movement permission to the right of the mart; it should allow you to walk on it, but there's an invisible wall there instead.
Devon Corp building has a tile error: when you walk behind the fence, the character sprite goes under the tile right next to the entrance.
Squirren's PokéDex entry has a misspelling: viscious instead of vicious and there should be a semicolon between cute and however. /grammarnazi
In Genesis Cave, you walk towards the west, however you exit in Mekong City, which is to the north. Just saying, it's a little awkward and doesn't match the map.
Right after you beat Jaykob, he vanishes for an instant, but when you step he reappears.
Entering the gatehouse between Mekong City and Eden Path on the left side of the entrances does weird things: On Mekong side, you end up on the right side of the rug; on Eden side, you end up to the right of the entrance in the wall.
In the Thames Town Research Center, after beating Garrid, everyone talks about you getting a fossil, even before you get it from the researcher. Also, a guy gives you a Moon Stone; after he does, the text remains up and doesn't go down unless you talk to someone else.
The picture in the research lab makes a noise when you press A on it, but has no text.
In Atalanta Plains, the gatehouse has a messed up tile: stepping up one step puts the character's head above the overhang.
Some ladder confusion in Vrai Cave; some that lead up are down ladders, some that lead down are up ladders.
The smashable rocks in the lowest level of Vrai Cave re-appear after being smashed when the character moves.
A PokéBall item on Gogh Cross doesn't have a script.
For some reason, 0x Awakenings appear in my Items bag after picking up a Paralyze Heal in Origin Well. (It vanishes and reappears every so often until you leave the cave.)
Max's conversation on Lion Way has a misspelling; fleeding should be fleeing.
Everything else I saw has been mentioned already. Sorry if I seem nit-picky. Everything else you have done is very impressive, especially the Fakémon. (By the way, could you have made Viscamans any more amazing? Awesome movepool + huge Sp. Attack stat = Best thing EVER.) I've played through the whole beta now, and I'm very impressed with the level of design you've put into this. The dead ends on the map do irk me, however; that's just personal opinion, though, so yeah. I'll just *sunglasses* deal w/ it.
Just a question, did you base Kaveri Town and Maas City off of the latter of the Sevii Islands (4-7)? If so, I think that's the problem with the HM Fly. It's just a hunch, feel free to ignore it.
Also, can I get some help finding the 'somewhat rare' Pokémon on Cynic Way? I understand that it is a shiny Larvitar from reading other posts, but I can't find it, and I'm pretty sure I've stepped on every single tile, tall grass or not. I'm not sure what exactly I'm supposed to do.