Under the troop recruitment section of the empire policy screen, there is an option to regulate the amount of troops the ai will garrison at colonies. I usually set this to "none" and garrison troops myself. However, the ai still garrisons troops and even un-garrisons the ones that I manually garrison and resets to its original garrison choices. I can't find any other options regarding troop garrisoning so I assume this isn't the intended ai behavior.
This happens because you have Troop Recruitment set to be automated in the Game Options screen. When Troop Recruitment is automated, all troop management at colonies is handled by the AI. Thus when you manually garrison troops, the AI will then follow your empire policy settings (no garrisoned troops), thus overriding your changes.
To manage colony troop garrisons yourself you must turn Troop Recruitment automation off.
Also, fleets will go and retrofit when I approve the prompt from the advisor, which is normal, but they do it even when there are no new designs to upgrade to. Every ship in the fleet would be the latest design. I should also note that the individual ships when not in a fleet DO NOT go for a retrofit when there are no new designs, as they are set to manual retrofit status. The ships on auto retrofit will queue a retrofit at the advisor prompt, but will cancel it after it finishes whatever its doing if there are no new designs. I only manually upgrade and retrofit military ships, while the other state ships auto retrofit. State bases and private stuff is on full auto and works fine.
Again, it's only when ships are in a fleet do they try and retrofit at the advisor's prompt when there are no new designs for them, and I don't recall this happening before Shadows. This can be very frustrating with multiple fleets, having to cancel each retrofit mission before they run off to a spaceport. This may have something to do with the problem of fleets not properly retrofitting when manually told to do so as a fleet, which was reported here a few days ago by someone else. Hopefully all of that made some sense. I'll try to provide a save file where these things are occurring.
Thanks for that report. This is fixed in the 188.8.131.52 update, which should be available tomorrow.