Has anyone found a fix for this? I was having the same issue with FaceTime - the same iCloud account was logged in on my iPhone and iPad running iOS 8 and my Mac running the Yosemite public beta. My number was showing up in iMessages on all three, but only on my phone for FaceTime - my Mac and iPad only showed email addresses. I frequently receive FaceTime calls that are directed at my phone number so I wanted to fix this. Oddly enough my iPhone number was showing up in Facetime's preferences for continuity.
1. In settings, go to Messages and turn it off iMessage
2. In settings, go to FaceTime and turn it off
3. In Settings go to iCloud and turn off Backup
4. In Settings go to iCloud and turn off iCloud Drive
5. In Settings go to iCloud and go to the bottom and sign out and select Keep on your iPhone
6. In Settings go to Phone and enter your original phone number keeping the + and 1 at the beginning
7. In Settings turn off WiFi and Bluetooth
8. If you have other devices logged into your iCloud account, repeat the previous for each device.
9. Reboot phone by holding power and home button at the same time until it shuts off, then power back on.
10 Once phone is back on, verify in Settings Phone that your original number is still there, if not change it again.
11 In Settings, sign back into iCloud
12 In Settings, turn on iMessages in Messages back on and go to Send and Receive and make sure your old number is checked and the new temp number is not checked.
13 In Settings, turn Facteime back on and go to Send and Receive and make sure your old number is checked and the new temp number is not checked.
14. In Settings go to iCloud and make sure iCloud Drive and Backup and back on
15 In Settings go to Cellular then Cellular Data Options and turn on Data Roaming
16. Repeat steps 11 to 14 for any additional devices