Part of the challenge is when results are so close. I think Brexit was 52% for 48% against (rounded.) It stands to reason, unless the thing voted on becomes a clear success in the eyes of most of the country, it will never be a settled debate.
The same will be true if there's ever another Scottish independence referendum. If it's close, and x years later the benefits are difficult to prove/quantify, the argument about whether it was worth it will go round and round.
For any referendum that is on such a scale of importance, might it be an idea to have a minimum % that's required for the proposal to be enacted? Perhaps somewhere in the region of 55-60% inc. That way, even if the success of the thing is debatable in years to come, it can be pointed out that more than a slim majority voted for said change.