When I was playing ZC recently, I found a couple ZC inconsistencies that don't occur on the original NES game.
1. CSet 9 doesn't update on screens that have pushable rocks or graves on the overworld. On the NES version, the level sprite colour is temporarily replaced with BG Palette 0, 2 or 3. Here's an example of what it looks like. The left is ZC, the right is the NES version.
2. Fast quitting while in a door repair room causes the guy to disappear without paying the door repair. This is not the case in the original NES version.
3. A few secret rooms in the ZC 2nd quest are missing. These are: A potion lady at screen 02 and a shop (type 0) at screen 15.
4. Boss palettes don't synchronise with CSet 9. On the NES version, the fourth Sprite palette (level colour) is temporarily replaced when you fight a certain boss monster (i.e. Aquamentus). This is easy to track on the NES version when you have the compass for that level. The second colour for the "dark" compass palette corresponds to the level colour. In ZC, the compass dark colour on NES-style quests is supposed to be 0x91 and not 0x00.
5. When you have the maximum rupees, it should only play sound effect 5 (Inventory).
Edit: Made a couple clarifications on inconsistency 4.
Edit number two: Found another minor inconsistency.