If you see an "ability missing" message when opening a deck in the Deck Builder it will likely* be because the deck contained abilities from the demo set that have since been removed.
"Demo set" abilities are available on cards in place of incepted, levelled abilities. They carry a points penalty (currently 20%) and won't ever be available for play in ranked games.
We regularly cycle demo set abilities to test new ability designs and card types. Incepted abilities are never removed.
When you load a deck that has had demo set abilities removed, the cards that contained them will still be included in the deck but the abilities themselves will no longer be visible. Saving the deck will stop the message from appearing again, but you may wish to add more abilities in their place.
*It's also possible that you would receive this message if you had submitted a deck directly via the (currently undocumented) deck builder API.
Demo abilities status (December 2017):
There are currently no deployed demo abilities. All hero cards now use regular incepted abilities.
If you had previously built decks using demo-only abilities in the beta you'll need to replace them with those that use incepted abilities.