As you can see there is no way to add the sector when a fleet is in the sector. Most likely when removing, too.
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While it's highly annoying and unintuitive, there is a workaround. You don't have to click on the plus sign to add a system to a sector, you can also click on the star (between the plus/ship icon and the habitable worlds icon) to do it.
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Edit: ok, it's nearly impossible. You can try to find a spot "far" away from the icons ... 
We are aware of this issue and it's already reported in our database. Thanks for posting!