Just downloaded the game and I very much enjoy what I have seen so far. Not sure if this was a bug or not but I found an unmarked hallway on floor 2 on Lulune's map. Also noticed the shop bug you mentioned. The stone Syr gives you does not show up in the inventory either. Not sure if my growths were unbalanced from my play style but my Agility went up by only 24, while my Dexterity was double that, and triple for the others. Out of curiosity does saying you love Aiz and "I like it just the 2 of us" to Hestia lock me into the Aiz/Hestia routes; I've just finished growth spurt and I'm aiming for Syr or Ryuu for the first go around. Fingers crossed for a potential harem or at least 2 girl ending.
Ryuu and Syr won't care about that choice, choosing that you do not like Ais gives you access to Eina's route, that is only because you literally tell to her face "I love somebody else", can't be good if you want to start something with her
Unmarked spots are not a bug, if you look at that spot, there are remains of a wall... It was a way to show how the dungeon keeps changing. Same thing happens if you head to the fifth floor after the tutorial (the path to 6th floor will be unlocked) or how the 4th floor will extend slightly after you gain access to the seventh floor.
The magic stone should always show, it is more likely it stacked with other magic stones or was sold shortly after (entering and leaving the dungeon will sell all your magic stones and treasure).
If that was a bug, it should no longer occur on R5.
Having more agility and dexterity than the other stats is how Bell normally grows in the original source, and how you will grow in the game unless you push for other stats (purposely get slapped around by monsters to increase endurance, or slay hundreds of monsters to increase your strength).