A negative invoice seems to be generated in the following situation:

1. A developer signs up and an application is created on a paid plan
2. The application is downgraded to a free plan
3. The cost is prorated, and a "Refund" line item is created for the invoice

Billing process tries to charge the invoice, but it fails with an error, e.g. in Braintree:

Amount cannot be negative. (81501)