I've noticed that when loading a game, linkReferences() is being called twice on every object. I'm just wondering if that is normal behaviour from EE or if my code might be causing it to call twice. Is EE supposed to call linkReferences() twice on each object?

I just tested this in the Object References tutorial and it is calling linkReferences() twice on the character object when loading. The first call works fine, i.e. links the desired_item correctly, so the second call just seems to be redundant.
Is this a bug in EE?

Hello,

That's normal behavior, the method can be called multiple times at initialization and later during the game in case new objects got loaded.