Hi, sometimes fleets will be off the center of a space. I am not sure if it does this with only one ship in a space though. Also, if I remember correctly, sometimes if I right click on the space the fleet will instantly switch over to the center of the tile. The game is on a small map with only the AI and I (there used to be another AI that I set to start allied with the other AI, and there are still some starbases left over from him). Also, I have the graphics settings set to full except for antialiasing which is set to x2, and I have vsync and fullscreen off.
My PC's possibly relevant specs are the following:
Windows 10 Home
EVGA Geforce GTX 670 FTW
Corsair 8GB 1600MHz Ram
Asrock Z77 Extreme 4