So I'm going to do my best to explain this bug, I also think this only happens if you have about 5 or more rune pages.
So oftenly it happens that after you finish a game, 2 of your rune pages you own will be selected for one reason or another.
now this doesn't add 2 keystones. Instead the game decides which one will be brought with you in the game. This can be really frustrating, hopefully this will be fixed soon.