Hi Johan,
This sounds like a reporting issue due to incorrect MiNT links or RF-Domain configuration. Is it a single-site or a multi-site deployment?
You can check mint links with the help of "show mint links" executed on the controller. If it's a multi-site deployment, you must have MiNT links (MiNT Level2) equal to the no. of sites + one link to the secondary/backup controller. For single-site, it's most probably MiNT Level1 and the no. of links should be equal to the no. of APs + one link for the secondary/backup controller. If the MiNT links are not properly set up (based on single-site or multi-site deployment) you will experience such reporting issues on the controller.
I would also suggest you check the RF-Domain managers on each site, use the "show global domain managers" command on the controller to check the elected RF-Domain managers. The no. of RF-Domain managers must be equal to the no. of sites.