Could not find this in the rules, but other than a house ruling, what is the accepted rule of what to do if you do not have enough miniatures during the build and deploy? Do you improvise or say the ship cannot be built?

You can only build and deploy what you have miniatures for. You MAY NOT proxy miniatures. (Page 6 Rules Reference)

COMPONENT LIMITATIONS

If players run out of a component type during the game, they should

obey the following rules:

Dice: Each player can roll a maximum of five black dice and

five red dice in each mission or attack.

Markers and Rings: Leaders and attachment rings are limited

to those included in the game.

All other markers are not limited. If players run out of a marker

type, use a suitable substitute, such as a coin.

Units: Units are limited to those included in the game. A player

cannot build a unit type if there are none available.

During step 5 of the Refresh Phase, a player can destroy any

of his units that are on the game board and return them to

the supply.

Cards: When a deck becomes depleted, shuffle the deck’s

discard pile and place it facedown to create a new deck.

You can only build and deploy what you have miniatures for. You MAY NOT proxy miniatures. (Page 6 Rules Reference)

COMPONENT LIMITATIONS

If players run out of a component type during the game, they should

obey the following rules:

Dice: Each player can roll a maximum of five black dice and

five red dice in each mission or attack.

Markers and Rings: Leaders and attachment rings are limited

to those included in the game.

All other markers are not limited. If players run out of a marker

type, use a suitable substitute, such as a coin.

Units: Units are limited to those included in the game. A player

cannot build a unit type if there are none available.

During step 5 of the Refresh Phase, a player can destroy any

of his units that are on the game board and return them to

the supply.

Cards: When a deck becomes depleted, shuffle the deck’s

discard pile and place it facedown to create a new deck.

Regarding destroying units and returning them to the supply, can this only occur when you have run out of units or during ANY Refresh Phase at 5? If the former, can you only destroy the type(s) of unit(s) of which you have run out or can you destroy any type of unit?

FAQ page 2. Basically when you have an opportunity to build a unit and have none in your supply.

...need more expansions for more units to build!...