I have seen this posted several times and it has happened to me twice.
When you colonize a planet and get the pirate warning on the same turn, the game freezes and you have to exit and restart. On the previous occasion I was able to avoid the freeze after reloading by stopping my surveyor until the colonization was completed.
As I posted elsewhere, the pirate anomaly is a neat little feature but it gets old after a few battles and it just become an auto-resolve click. If the feature is going to be in the final release, when there are real pirates in the game, maybe you might consider turning off the anomaly pirates after 40-50 turns. They are just a pain in the ass (no fun) to deal with throughout the entire game.
If they are not going to be included in the final release, if it were me, I would get rid of them in the next patch. When you consider all the bug reports on this item it doesn't seem worth it for a temporary feature.
If you need me to submit a ticket on this let me know. I am going to restart the game after this post so let me know if that will affect the dump or whatever I need to send.
Y'all are probably on this one already based on the number of posts I have seen on the problem.