What happens if I unlock a Pokemon I already have?
When unlocking a Pokemon you already have, you are refunded the amount of coins that would be used to get that Pokemon. So don't be afraid to spend your coins on unlocking Pokemon that may be available through other means at a later time.
NOTE: It is important to note that this only applies to Pokemon, not items, and if you spend Aeos gems to unlock a Pokemon, they are not refunded and you still receive coins instead.