I don't think they told us which bones they were. It is a conspiracy. Could be the pope could be a bishop could be a violent criminal.
The simple answer is: we dont know whose bones they are. How did they get there? They were buried there.
That's all we know. Over the last two millennia many people have been buried in or around churches, there is nothing mysterious or conspiratorial about it, it is a fact. Sometimes royalty or nobility, sometimes clergy or martyrs and most churches have a crypt underneath. Some thought they would obtain a blessing by being buried there.
In south America I visited a church where skulls were arranged in a pattern under the church, as were thigh and other bones. It was near a centre for the Inquisition and so there was some speculation that these were the bones of victims but we had no way of knowing for sure. One thing that is certain is that we must be careful of making assumptions without real evidence.
No one knows at this time. One day the books will be opened and we will find out, the wrongdoers will pay for their crimes. And it will all be overseen by Him who see and know everything. At this moment the truth is hidden from us by the great Apostate who thinks he is God.
Same as all secret sins...