Hi!
A few questions first:
- Are there any categories excluded?
- Are there any category filters selected on the frontend?
- Are there any other filters, like custom field or taxonomy visible?
- Is there anything else excluded in the configuration?
- Are the posts statuses published?
Excluding things along multisite is usually not a good idea, because terms unfortunately are not shared along multisite installs, thus have different id’s. So two posts on separate multisites under the same category name are not actually under the same category and are not possible to filter because of that. Same goes for custom fields, taxonomies etc.. I’m hoping version 5 of wordpress will provide an interface for this.