I'm cross-posting this from a response in the Bugs sub-forum to improve visibility on this change.

During the initial design phase of the UI update for Collection, the TPCi team indicated that we would prefer to see the quantities for an item displayed as Tradable/Untradable, rather than Total/Untradable. For example, a player has 3 tradable and 2 untradable Yveltal-EX cards in her collection. Under the previous implementation, it would have been displayed as Total/Untradable, or 5/2. Under the requested implementation, it would have been displayed as Tradable/Untradable, or 3/2. The total number of cards remains the same, it just doesn't require the player to do math to determine how many copies of Yveltal-EX she has available for trade.
In short, when looking at an item in your collection, the sum of the two quantities you see now should be equal to the quantity that was in the left/blue container prior to the game update.

If you believe that you are missing items after yesterday's update, please use the link in my signature to visit the support portal and create a ticket with a list of the items you believe are missing.