For reference it's on P28 of the rulebook
Tokens and plastic ships are limited to the quantity provided,
and can run out during the game. The current player always
decides the order in which a component type is placed, and if
there are not enough, he decides which ones are not placed.
Example: A Cylon attack Crisis Card is drawn that requires
two basestars to be placed on the game board. There is
already one basestar on the game board, so there is only one
more that can be placed. The current player decides which of
the two basestars listed on the Cylon attack card to place on
the game board.