You are sure all the Creepers are dead?
Try to repair the game.
(Origin > Game Library > right click MELE > Repair)
(Steam > right click at MELE > Properties > Local Files > Verify integrity of game cache.)
I have this same issue, but I also noticed that as soon as I shut the door on the Geth ship arm, I was no longer able to save my game. So, I cannot proceed, nor save my game anymore.
@destal If you can't save, then the only thing to do is quit and reload.
Having said that, please make sure your C drive isn't too low on space: a couple people have reported that they can't save their progress when their system drive is too full. If this is the case for you as well, it's possible that clearing some space will help, although perhaps only after you restart your computer.
