Hi,
By default, the phone number is a custom field of the table "address". You can check this in the Display>Custom fields.
And since it is tied to the address, it is displayed with the address based on the "address format" you can configure under the "Checkout" tab of the HikaShop configuration.
By default, the "address format" takes into account the phone number associated with the address. So, by default, you should not have that issue.
So, either you're using another field to gather the phone number, or you've customized the "address format" setting and removed the piece of code there which takes into account the phone number custom field.
Please check these.