---You can ignore the beginning of the post; I organized it at the bottom, but I didn't want to delete the unorganized section in case it might come in handy---
I don't know if this counts, but the first time you talk to Crono's mom outside of the forced conversation she gives Crono's allowance for the fair...
Also, do layer things count? Not like people are going to be constantly turning off the layers unless they're doing it purposefully to find errors...
I'll list them in case (stop me if you don't want them so I don't keep doing it if it's unnecessary):
-In the Truce Inn, the left-most bed, without BG1 Layer, has some swords and a light (looks like it's from a wall from somewhere else)
Also, isn't Crono supposed to start with super-weapons and techs?
-Neither of the people in the residence in left Truce talks (empty dialogue box)
-If you walk to the left of Fiona's Shrine in the worldmap the shrine is half-over-half-under Crono
-World map says 1,000A.D. (is it even possible to edit that?)
I'll edit with more bugs and stuff
EDIT: I'll make this a list for easier reference:
Game/Conversation Errors:
-Crono's Mom gives Crono 200g for the Millenium Fair the first time you talk to her after she gives the 'assignments'
-Neither of the people in the residence in left Truce talks
-Mystic thing in Fiona's Shrine has a delay between pressing A and starting the dialogue
-Dude at the entrance of the Cathedral says that the Arboretum is on the 'left', wouldn't it make more sense to for it to be 'my left' or 'your left', since he's facing the opposite direction?
-There's some kind of pair of invisible barriers near the pole at the entrance to the main Cathedral room (walk into the main room, come out, and you can't walk directly to the left or right)
-The Porre Barracks still say 'Mayor's Manor'
Visual Errors:
-The Save page of the menu is messed up... the titles of the chapters of the saved games are on top of everything else... for example, when scrolling between pages of the menu, the 'No Save' thing is above the window with the page icons, and the "The Millenium Fair" is above the window for "Erase old save.. yes.. no"
-If you walk directly to the left of Fiona's Shrine on the World Map Crono will be half over/under the Shrine
-You can walk over the tops of the trees near Fiona's Shrine
-If you walk into the gateway in the Cathedral (the first door directly infront of the entrance) Crono will start to walk over the top of the gateway
-When you leave the main room of the Cathedral you end up in front of a pole, just seems weird that you can't go back and forth and have to go around a pole each time (or, there should be a pole in the exit of the main room too, rather than just the simple entrance from the original)
-You can walk above the corners of the wall near the exit of the main room of the cathedral.. it's easier to see than it is to understand explained
-If you walk a bit below the lowest-leftest bench in the main room of the Cathedral (so that Crono's hair just touches the bench) Crono is behind the bench, it also stays that way for a fraction of a second if you get closer to the bench, but after that it gets normal
-Column on the left wall of the Cathedral is non-existant, and works like the bench (with Crono being behind it)... note that Crono only ends up behind the column/bench if he approaches it from below it
-The grave-thing (what's it called... ugh) at the top of the Cathedral is always on top of Crono.. Same thing applies for that pedestool thing on the right (is that guy praying the guy who ends up with the Masamune?)
-If you walk up to the curtains in the main Cathedral room it looks messed up cuz Crono is in front of the wall, but behind the curtains
-In the conference(?) room above the main Cathedral room a piece of the small stairway at the entrance is above Crono
Hidden Visual Erros:
-(BG3 Layer) Sword/Lamp are hidden behind the left-most bed in the Truce Inn
I'll still edit with more stuff as I explore..