The reason for the problem that you describe is that the Aspell spell checker dictionary is different from the WordNet dictionary. As you can see the WordNet dictionary is usually a superior one. We use predefined Aspose dictionaries from reliable sources, but it might be that they are not complete or need updates. Meanwhile you can add the missing words manually, or add them to your custom dictionary.
I went to the SCOWL site at http://app.aspell.net/create. I only used American spelling, but included level 3 spelling variants, both special lists, and the “insane” size. ~350k lines in the word list.
Scrivener v3 uses Hunspell, Scrivener v1.9 uses Aspell. Mos likely you have followed v1.9 instructions, which do not work for v3 Beta. Check the forum, some users reported URLs with useful Hunspell dictionaries.