That happens in any system where you don't have all the information. This question applies from both directions. I'm not sure that this has an easy answer. Somehow we manage. I'm not going to say that there isn't something else to thought or consciousness, but if there is, it's not readily apparent.
Nobody has that answer.
I wonder if there aren't several distinct processes at work that lessen doubt. Finally, there are thought processes and ideas that we can generate that allow us to rationalize the events observed. The first two processes are ones that we might all realistically be able to share. The last can be highly individualized. I think that is where we might split on opinions.