I never use hyphens where em dashes would be correct.
I do have issues determining when a two-word phrase should or shouldn't be hyphenated. It surely doesn't help that I grew up in a bilingual English/German household, so that my first instinct is often to reject either option, and fully concatenate the two words instead.
(Whether that last comma is appropriate opens a whole other set of punctuation issues ... and yes, I do tend to deliberately misuse ellipses for effect.)