This happens sometimes, when an NPC opens a door that transitions to load screen what you do is you simply look away from the door so that you don't see the activate button. It can take a bit like 3 seconds but after that you should be able to use the door.
Try reloading a previous save. I had to do that with this quest because at some point the eyebot became stuck.
Also, what Gamefever said. Sometimes when an NPC walks through a door it temporarily becomes inaccessible.
I've found that my girl needs to look above the door to see the activator quite regularly.
Please do not post Spoilers or Quest Details in General
Moving this now