Sometimes the game will completely freeze, and the ships and timer will also freeze (although it is still possible to interact with the towns.
Talking to the Architect in town and accessing the Build grid seems to unfreeze time, though the bug might still recur.
When a player reaches a certain rank, building names over buildings disappear.
When a shipyard has more than 1 ship to offer, it frequently auto-selects the 1st ship. Players could accidentally buy the wrong ship if they are not clicking the buy button fast enough.
On version 1.1.2 quests aren't giving any reputation increase.
Reportedly, loading a game will not allow saves to be made automatically.
This can be fixed by starting a new game, and then loading the save game again.
Autosave timer can also be adjusted by going into the Options.cfg in %APPDATA%\Kalypsomedia\Port Royale 3\
%APPDATA%\Kalypsomedia\Port Royale 3\
There is a section where one can adjust the number of seconds between autosaves:
Timer = 480