I personally suspect it's the dichotomy of directly elected president or a chamber elected symbolic president which functionally is what the governor general is. Basically the republican vote was split while the royalist vote was clear behind one outcome.
I voted for a republic. I wouldn't have, if the intent was to make it a direct election. I prefer the bicameral chambers to do it, a symbolic minor depoliticised role is better to me, than a standard strong popular elected president.
Also, referendum being expensive there was another question about a preamble to the constitution recognising aboriginal Australians. Again, this had divided support because of (in my personal opinion) a dishonest claim it discriminated between Australians. Two questions has some evidence causes higher no votes to both questions than one simple question.