Duplicate Contact Problem
You need to set the deduplication rule to match what you need. Not sure I completely understood your use case, but it seems that you have included the phone number on your default unsupervised dedupe rule?

Check this chapter in the book if the dedupe rules are not clear for you yet, it's powerful, but takes a while to use them properly and a common source of duplicates being created.

https://docs.civicrm.org/user/en/4.6/common-workflows/deduping-and-merging/