This is indeed a situation where a lot of information is missing in my experience. The few times I had denied boarding:
- on a connecting intercontinental flight I upgraded to J with miles for the long leg. KLM apparently forgot to re-instate the feeder leg that was with a partner airline. I still could do OLCI with the feeder or KLM, forgot whom. Gate staff refused to board me since according to what they saw my feeder ticket was not active. But of course this was explained in clear terms, led to frantic discussions and calls to KLM from both sides, and was solved just in time.
- 1 time I accepted re-routing due to overbooking. And of course there was clear explanation about my rights, compensation, and how I would be re-routed.
- 1 time with a CDG connection my feeder was delayed. They claimed I would miss my connection (not true, but that is another story), used my seat for someone else, but of course in the same email message they indicated how they rebooked me.

As others stated, it is inconceivable the reason for not being allowed to board when you have done OLCI is not communicated by ground staff. Denied boarding is a big thing and of course they should tell why it happens. And in the first case I mentioned, I made d*mnd sure the gate agents understood that from my perspective I had a totally valid ticket, consequences would be enormous if I could not take the flight (compare the missed car hire), etc. It is difficult to understand that OP did not set up such a discussion him/herself.