Steps to reproduce:
1) make sure you have organization, e.g. org A
2) switch to org A in context selector
3) go to domain
4) create a domain assigned to org A, this might still work
5) try to create new one again assigned to org A (should be preselected since you're in its context), it will stuck on the creation form displaying no errors and you can find "Failed to save: Taxable taxonomies is invalid" in log (if you have at least info level enabled)

to reproduce from console

# make sure there's at least one Domain in Organization.first
Organization.current = Organization.first
d = Domain.new :organization_ids => [1]
d.valid? # => false
d.taxable_taxonomies # return invalid taxable taxonomies linked to other (existing!) domain

Cause:
It seems that default scope added by taxonomies registers ids of existing records which gets picked by https://github.com/rails/rails/blob/v4.2.7.1/activerecord/lib/active_record/scoping/named.rb#L39:AR when it creates associations. A workaround is to do Domain.unscoped.new