This is definitely a missed error (because as a module item it should be . not ~ there):

And about this I'm unsure:

The references are good so perhaps it's just Umberto failing to render them. (see https://github.com/ckeditor/ckeditor5-dev/issues/228#issuecomment-308042049)
cc @m-turek
About the second issue: Umberto doesn't support shorthands like {@link ~Classname#methodName}, it expects a full reference like: module:x/y/z~Z. I wasn't aware of a shorthand format. So I'd have to add support for it to make it work.
I thought so. Could you report ckeditor/ckeditor5-dev#228 and ckeditor/ckeditor5-dev#229 for Umberto so we can track these issues (both of them can be handled separately from issues in this repo)?
It's fixed.
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It's fixed.