I have a regular Glaceon ex, a 1 star, and a shiny, but in deck-building mode, my collection only lists 2 Glaceon ex. A similar thing happens with Yanmega ex, I have one copy of the shiny, but in deck-building mode it says I don’t have any copies at all.
This doesn’t happen with Marowak ex, Wigglytuff ex, or Gallade ex, so it’s probably limited to Wisdom of Sea and Sky’s shinies.