I think that you might be jumping the gun a bit. It is so hard to grow a pristine orchid without little issues here and there. Fungal or bacterial soft rots would take hold and spread rapidly.
Other diseases in my experience never start out and stay so small. They start to spread and get bigger.
I don’t think it is a virus. That should be noticed on leaves or flowers first.
I would just watch all of your plants on a regular basis. And in doing that, not every spot or mark is serious.
Diligence is always a good idea.