I have picked as an example of an ontological dispute the argument over whether there was something before the Big Bang. I am not a scientist and therefore my post will focus on the ways we might approach the question.
There are a number of competing theories about what happened before the Big Bang. It is unlikely (impossible?) that all of them are true. I conclude from this that we can formulate concepts which don't exist, if by exist we mean exist in space and time. But the concepts which turn out to be non-existent are not necessarily meaningless.
To be given serious (scientific) consideration, each hypothesis needs to be coherent and not contradicted (falsified) by experimental evidence. It is this coherence which allows the concept to have meaning, an incoherent or self-contradictory theory is either false or meaningless.
Many scientists believe that the Universe began at the Big Bang, estimated to have taken place 14 billion years ago. Was it at that point that space and time began? Some argue that there was nothing before the Big Bang. But it seems odd (incoherent?) to describe a scenario where there is no "before" (just as it is odd to think of no "after"). Kant would argue that our ideas of space and time are essential to our understanding of reality, I am inclined to agree with this view. I therefore instinctively reject the idea of a beginning of space and time as incoherent.
But is our idea of the existence of space and time dependent on the existence of light? If there was no energy before the Big Bang, and no light to travel at lightspeed, would there still be time? Does our idea of time require distance and speed to have meaning?
Modern science has developed theories about the "time" before the Big Bang by using quantum physics. But even if we devise a theory which gains widespread acceptance, does this mean we would regard it as "true". In the absence of time travel how would we know?
My final comment is that some people prefer a supernatural explanation; for them, some questions are not answerable scientifically.