I've had the same problem. I tried operating a gravity generator both on top of my ship and inside it, and in both cases I was sent somewhere from 200m - 400m away from my ship, while still being affected by the gravity. Since I was still in space, though, I was unable to move and float back to my ship, so I had to restart the game and respawn to fix the issue.
As a side note, I made sure the generator was properly oriented, so that wasn't the issue.
I hope this is fixed soon, I would really like to get to use these gravity generators properly!