You're probably also giving that out to businesses you have a relationship with. And most people don't have a second fake phone number to give out to avoid matching.
It's a bit like grocery store loyalty cards: you can give the grocery store bogus contact info when you sign up for one, but the first time you swipe a credit card to pay for your groceries, the store gets your name and a unique ID linked to you (the card #) that can be used to match your profile in (say) an Acxiom database.
I'm curious why Facebook would link a shadow profile about you to your real profile though, even if it knew with relative certainty you were one in the same. I can see no benefit other than advertising (which doesn't really necessitate them telling you in this way) but it seems that it could pretty easily lead to the misunderstanding above where folks impugn nefarious motives to Facebook that aren't accurate.
E.g., they know you'd like them to assume that [email protected] is your email address (and they do you the favor in all publicly visible parts of your profile), but they also see that most of the people in your friends list haven an entry for "[email protected]" in their address book, filed under your name. So they'll simply add both addresses as keys to your account.