In the update we released yesterday (December 12th), there is a bug where skill shards do not properly affect characters in combat in certain situations:

What Causes the Bug: While on Auto-play, skill shards do not function.

As a temporary work around, you can do auto-play grinding on an earlier battle in the world you normally grind, or can play normally with the full benefit of skill shards by manually playing levels.

Skill shards will return to properly affecting in the next update, which we are working to submit as soon as possible.