if a person is in the same 'loaded section' of the map as the enemy, they will activate/spawn and attack what they find. If you are in your friend's map segment, it really should fall to you to defend their base. Or have a communal base. Or make sure you are all far apart and stay away from each other. Or build your bases to be unreachable. The long and the short of it is: you can work around the issue, if you want to talk out how best to approach it with your group. Whether there should be a better mechanic in the game for this --- there is a suggestions page over there ->
but I am not going to get into the what ifs, just the what-is.