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What is the first hint that we get in the Matrix series that Neo wasn't the first and only 'One'?
My gut instinct is in the Chateau scene, when The Merovingian says these two lines:
Your predecessors had much more respect
...and
Mark my words boy, mark them well; I have survived your predecessors, and I will survive you!
The first movie details there being at least one prior "The One" who set "the first of us" free. Morpheus explains this to Neo shortly after the explanation of the real world -- the battery scene and Neo vomiting.
MORPHEUS: When the Matrix was first built there was a man born inside that had the ability to change what he wanted, to remake the Matrix as he saw fit. It was this man that freed the first of us and taught us the secret of the war; control the Matrix and you control the future.
However, as for there being multiple prior 'The Ones' I believe you may be correct.
Also, when Neo meets the Architect and all his predecessors are displayed on screens, the current Neo is the only one that is not surprised to hear the Architect say "that was quicker than the others", all the other versions of Neo lose the plot.
And if every version was quicker than the last leading to an exact repetition of the events up until that point, it is significant that Neo does not react: it means that this iteration of the Matrix is fundamentally different from the others.
When Morpheus tells Neo that he is not the first but a sort of reincarnation of the One in the first movie, the pattern is different from all other iterations where Neo only became aware of his predecessors when he met the architect.
