How to recreate:

1. Create a new creative world.
2. Put a map and paper in a crafting table or cartography table it to create a zoomed-out version of the map. Don't take it out of the table yet!
3. Note that the map in the output has the same ID, scaling and level as the original map.
4. Click with the middle mouse button on the map in the output to get a whole stack, and put it in your hotbar. Note that it still has the same ID.
5. Now click with the left (main) mouse button on the map in the output to take it out and put it in your hotbar. Note that it still has the same ID.
6. Close the GUI, and view both maps. The stack that you took with the middle mouse button is the same as the original map, while the map you took with the main mouse button is a zoomed-out version.
7. Open your inventory. The ID of the map you took with the main mouse button has now changed, the other hasn't.

Edit: Added screenshots to show the ID's