Yes, I am having the exact same issue after updating to 13.3.1 and was no longer able to deploy my app to my device. When I went to verify that I should be able to as a developer with a free account, I see it states it clearly on Apple's website that it says I should. https://developer.apple.com/support/compare-memberships/ Under the 'Who Should Enroll' title it states "You can learn how to develop apps for Apple platforms for free without enrolling. With just an Apple ID, you can access Xcode, software downloads, documentation, sample code, forums, and Feedback Assistant, and you can test your apps on devices."
Whether this is a bug or issue, I am trying to find out. I am hoping that Apple have not revoked this ability as it it essential for my project.
The only workaround that I have just found and do have some undesirable side effect are to roll back to iOS 13.3. By doing this I was then able to deploy my app to my iPhone however I was unable to restore my backup without it requiring to update. Most things on my phone have their own backup and most of iCloud data stays intact however you have to reinstall everything.