Scenario: I configured a "WYSIWYG" input format for a new Drupal 8 site I'm building. Having installed the entity_embed.module, I then wanted to add a button for embedding entities (natch) into content via the CKEditor toolbar. I added the necessary buttons and added some filters to this input format, and saved.
Proceeding then to add a new item of content with my freshly configured WYSIWYG, I was dismayed to see that half my toolbar buttons were missing. After a bit of rummaging around, it transpires that you have to be a bit careful with the input filters.
Solution: If you have the "Display any HTML as plain text" filter enabled, this strips out (or disables the functionality of?) certain of the toolbar buttons. Disabling this filter, saving the format and refreshing the "Add new..." page restored the buttons to their expected state. I'm sure this is by design, though it might be quite easy to overlook.
I got a clue from https://www.drupal.org/node/2598070