What I've already done:
The loot tables on my world are modified, however, I did not configure Golden Apples in the loot table for Magma Cubes.

What's happening anyway:
Size 1 Magma Cubes drop Golden Apples when killed. Sizes 2 and 4 drop the correct items as configured in my loot table folder. After testing in a different world, I found that this only occurs with my modified loot table, which I've included. Some of the other loot tables have been edited, if necessary I will attach them on request