The same thing happened to me.
Jetpack doesn’t automatically add a subscriber popup to your site without your permission.
It does, actually. It’s the newsletter subscriptions. It was enabled on both my blogs without asking me. I detest pop-ups on websites so I was quite horrified that Jetpack had added it to mine without asking.
It would be great if the Jetpack team could commit to not adding new features without making them opt-in rather than opt-out.