When the pilot of the craft is a military officer, he will route the information as specified in the SOP and then keep his mouth shut as specified for certain topics as specified by the SOP.
Civilian personnel on the ISS are sworn to uphold the communications rules; otherwise, they would not get a seat on the mission.
Some people, not many, will honor their promises. Astronauts are "pick of the litter" people, already well known for outstanding qualities.
You have explained the secrecy—however the notion that higher ups at NASA ignore UFOs strains credibility—it is much more likely they have a compartmentalized sub-group that deals with it.