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Can I say,

(a) Bats come at night.

(b) Bats come out during / in the night.
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a) sounds as though you were referring to a particular spot: Bats come at night to eat the fruit we put out for them.

b) "at" would be my first choice for a preposition in this sentence as well: "Bats come out at night." This means that bats are nocturnal animals; they leave their caves (or what have you) at night.
Comments  
Can I say,

(a) The bats come at night every day.

(b) Bats came outside in the night.

(c) The bats come to find food every night.

(d) The bats come out in the night.