Specific case when Berenice is in play
The Cities rules say about "Debts" (on page 4):


  Important: monetary losses are always resolved at the end of a turn, after players have played their cards, possibly having paid for trade and/or obtained money...


So Alice takes 4 coins (3 + 1), and then she decides whether she wants to 


pay 3 coins, 
pay 2 coins and take 1 Debt token,
pay 1 coin and take 2 Debt tokens, or
take 3 Debt tokens.