It seems that if a significant change to a sector a player has logged off at that has occured while the player is logged off will cause them to timeout when attempting to reconnect to the server.
It might have something to do with the way StarMade is handling the download of data when the player is trying to load it, I am not sure how your connection handler is working but it looks like when a player is reconnecting to a server and it has had a significant change, the player will attempt to download that data when they load the sector but it seems that this download is either too slow, or is hanging completely, eventually causing the connection to timeout.