Honestly, if it were doing that it'd need to be a workflow or formula of some kind, and you would see the result in the Contact record just by looking in the page layout as well. So if you can't see that, it's unlikely. Reports are just a reflection of the data in the field. It's more likely you have multiple "phone" fields and you've accidentally go one rather than the other showing in your report.
Salesforce reports are tricky to troubleshoot without actually seeing the report though.