I think the cause of this issue is how often the game checks to see if the ship con colonize, if you wait long enough it's been my experience that it will colonize, just not as soon as it can. For example if when you enter a grav well and you can colonize the auto cast will activate and the ship will proceed to colonize the planet; but if you don't have the tech or the antimatter, then it will take a little bit after you can colonize for the game to realize it needs to send the ship to colonize.
