I'ver had white spot on my koi in my quarantine pond a couple of times. It's not that rare at all but you don't always see the white spots and have to do a scrape to see the parasites under a microscope.
I'm puzzled why White spot has even been mentioned though as fish losing scales is not symptom of it.
Is agree with the idea that your koi being in a glass tank is getting startled and crashing around which knocked some of his scales off. His crashing around is likely to knock into the goldfish in such cramped quarters (compared to a pond that is) and startle them which has probably caused their scale loss. Covering the tank is probably well worth a try and good advice.