The IRS has been cracking down on identity theft for the last several years. This is a great thing, because a lot of people were becoming victims of tax refund identity theft.
However, a lot of people think they are "verifying their identity" when they call the IRS. And while this is true, it's not identity theft related.
Whenever you call the IRS, they will ask you to verify your ID. This is just for your security, and is designed to prevent identity theft. It doesn't mean there is an identity theft issue with your return. Many callers have reported IRS representatives saying this is "to protect your identity", and that's correct - but it's not because there is a problem with your return.
If you do have an identity theft issue with your return, you're going to get a form 5071C letter in the mail from the IRS. You'll also be asked to verify your identity in person at an IRS office, or through a new website setup for identity verification, Identity Verification Service.
So, unless you had to do that, identity theft did NOT impact your return.