End point returns different results for company-managed and team-managed projects

We are seeing an issue where our customers using team-managed projects don’t see all the issues on their sprints when using the /rest/agile/1.0/sprint/${sprintId}/issue endpoint.
Company-managed projects return a collection with subtasks, but team-managed projects don’t return the subtask.
/rest/agile/1.0/board/${boardId}/backlog returns the subtasks but not the user stories in a sprint.

Furthermore, a jql search on the two types of projects using search=sprint{number}, will return different results.

This change between company-managed and team-managed is not documented. We are using connect with project admin permissions.
Is there any workaround or existing solution?