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The Rules wrote:
In the lower right corner of the game board the
buildings are placed: Inside the upper three lines
6 factories each for sugar, gold, and spices, and
inside the lower 2 lines the remaining shipyards
and churches from left to right (with more than 2
players, the most expensive fields are left free).
So with 2 Players all places are filled, with 3 one each stays empty, with 4 two each and with 5 players three places in churches and shipyards line stay empty.
Or as listed in the rules, you should have 10 churches and 10 shipyards in the game.
If you have less contact the Publisher.