Just to quote an announcement from the discord channel -
"Hello everyone,
there is a potential issue with the summing of Incarnates since the last patch. If you have disabled "add skills" in the Gameplay options (it´s related to the hotbar), your Incarnate might lack certain skills. We are working on this, but until it is fixed please use the following workaround:
1. Let your Incarnate die.
2. Go to Gameplay Options.
3. Enable "add Skills".
4. Summon a new Incarnate.
This should solve the problem of missing skills.
IMPORTANT: You need to make sure the incarnate is dead before summoning a new one once you enabled the option again."