Hmm… Did you by chance attempt to manually add
wp_head() to the theme because of that silly nag that Jetpack gives you?
I’ve seen this nag at the top of people’s WP Admin. I think it’s from Jetpack, but I can’t remember for sure. However, if you did indeed add
wp_head thinking the theme didn’t already have it, that would explain why you’re getting duplicates of all this. I can’t think of any other logical explanation.