No, the AI cannot build more than legally allowed. What has happened is you have captured a planet from a race with the "Advanced Storage Techniques" ability. The AI had filled it to capacity, which is higher than normal because of that special ability. Since you do not have that ability, the planet now defaults to the usual number of facilities. If you can use the facilities, enjoy the extra capacity.
If you have to scrap some of them, you will not be able to recover those 'extra' slots.