I don't think all variations are mistakes.
I personally never felt the green waters were mistakes; they are just how the water looks after the algae moves in. I have seen pictures of the same lighthouse where the water was blue and the same lighthouse with green water.

Lightning rods were just a design change where HL felt that the lighthouses were better off not to have the wire rods. Even though we all like the lightning rods better, it only makes sense that figurines should not have a wire sticking out of their tops.

Many variations where caused by manufacturer change. It was not a mistake; it was just changes created by using a different company.

I guess we could call the miss-spelled versions a mistake, but I doubt that HL would do a willfully variation like that.