Heya DarkBloodbane, thanks for playing some more! This is really helpful.
1. The key purchase was indeed a bug, thanks for catching that. You could only buy keys if you had more than one already, which I'm surprised you happened to have when you bought them on the other spots. You should be able to buy keys once I post the update (shortly after this post).
That said, you really shouldn't need to buy keys. They were added sort of as a scapegoat in case I messed up a puzzle design in a dungeon so the player was never locked from progress, but in theory you should never need to buy keys. Dungeons have either the exact amount you need or sometimes an extra one or two.
2. You can't get the shield because you already have it, in fact you have it equipped in the picture. The first two shields are volatile, they can be lost, which is why there's more than one place to get replacements. (You just happened to find the one that's free!)
3. The jumping enemies were fixed in one of the updates. Once you update they should behave properly. If they still do weird stuff after an update, please post a screenshot of the room they're having trouble with, it would be greatly appreciated.
4. The time stop will temporarily disable any enemies that can become invulnerable like the Wizzrobes (wizards), Leevers (burrowing enemies) and Zora (fish guys). This is intentional as otherwise they would be frozen in an invulnerable state and you wouldn't be able to progress. They don't get killed however, just disabled, so returning to the room resets them. This is intentional.
5. I've tested this and found no issues. To clarify, only the Master Sword can destroy the white rocks. Were you using the Wooden Sword perhaps? The rock next to level 5 should work just like the others.
Again, thanks a lot for playing! Since you've progressed quite a bit, what are your thoughts so far? Also, if you have a rough estimate of how many hours you've played, would you mind sharing that?