I'm having the same issue and its driving me crazy. I just did a factory restore not to long ago because I had a software bug on my iPhone 4 and the only way to get rid of it is to set it up as a new device which sucks because I lost all my game data even though it was synced with iCloud. It was so nice to have those annoying "other + number" gone but of course I have new ones now.
I thought it might have been because of the contact backup app I use but its not and I've tried everything suggested bit none of it works so I guess I just have to live with it even though I have tons of numbers there from texting people on Craigslist, fun stuff.
I did want to tell you that the contact backup app I have is awesome and thought I'd share it with you because you can even download the app to other devices that have Android and copy all your contacts with all their info and even contact pictures on to the device.
It's called PhoneCopy. Every time you add a contact, change the contacts info, picture, even delete a contact, etc then you just to to it and it shows how many changes have been made and hit sync and it takes a few seconds and its done! None of the emailing the contacts to email address. You do have to set up an account but its really easy and its great! I even put it on my dads iPhone and told my boyfriend he should put it on his that's Android and its a good thing he did because he had to switch to a new carrier and all he had to do was download the app, login, sync and ta da! Even though I have my contacts backed up else where as well I don't sync them to there often so this is my safety net. The only thing that I don't like is when you added them back on an iPhone the contact picture is really small and at the top but if you go to the contacts with pictures just hit Edit Photo and when it pulls up just save it and its back to normal size. I guess it's done that way incase you have a lot of contacts to save room but over all I think it's worth it.
Now, I just hope we can fix this annoying deleted numbers issue. Blah!