If you are syncing whenever you open the app on a device, and syncing when you close/leave the app on that device, you should always be working with the latest version of your collection. Cloud Sync - AnkiMobile Manual
After syncing your iPad, try checking AnkiWeb directly through the website interface – Cloud Sync - AnkiMobile Manual – and verify that your changes from your iPad have reached the servers. Then sync your iPhone. At least that will narrow down which device is having the sync issues.