It's far from being obvious how included resources and pagination plays together. It should be clarified in the specification itself.

It links many complex topics:

1. Relationship URLs
2. Resource identifier objects as primary data
3. include query parameter and relationship paths for relationship URLs

For additional context, please see this recent question in the forum about it: https://discuss.jsonapi.org/t/where-to-put-pagination-links-for-included-collections/2885