Some contacts not displaying but are in call history and on Whats App

I think this happened after upgrading to iOS 6, but some contacts which were on my phone are no longer displaying in 'My Contacts' however when I type the number in manually they appear. They are also listed in my Whatsapp contacts so I know they are no my phone.
I have also tried checking for them on iCloud.com however they are not there either. I have also gone to contacts Groups to make sure it says display all contacts which it does.
The biggest question here is I had this problem on my 3Gs and have just got the iPhone 5 and the same issue has happened here?!?!
REALLY STUCK HERE, HELP PLEASE!!!!

Problem solved.  When a contact is added on your iPhone, it doesn't necessarily go into iCloud contacts.  They can go under contacts for any email you have on your phone if you have "contacts" toggled "on" under settings.  Backup your phone. Then restore your phone to an old backup from prior to having problems.  After that, turn off iCloud contacts on your phone, and delete them from your phone when asked.  Look to see what contacts remain on your phone and add those to your iCloud.  If you have a Mac computer, just email them to yourself when you go under each one and hit "share contact."  Then, on your Mac, open the email and click on the ".vcf" attachment and it should put it right into your iCloud contacts.  Then you can restore your iPhone back to your original backup.  Go under your "Mail, Contacts and Calendars" settings and turn off your contacts for any other emails if you want to (not sure if you will have duplicate contacts if you don't).
Don't forget to make sure iCloud contacts are "on" when you are done- it may take a while for all the contacts to get back on your phone- I shut my phone off and restarted it also.
Good Luck!

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