If anyone else has this problem, the solution turned out to be relatively simple. The card we were using to test had incorrect metadata attached to it and therefore our card did not have the associatedApplicationIdentifiers set correctly. If you have the "Getting Started with Apple Pay In-App Provisioning, Verification & Security (3.0)" document, see section 5.4. "PNO Pass Metadata Configuration" for more information.

I am also having this issue, but I don't know how to solve it yet.