Security deposits are never charged at the time of booking. They're only charged if there's any incidents and need to make a claim. Some guests get confused and think that the security deposit is included in the overall rate when they book. I've had this happen before.
Example
Guest is booking 3 nights for a total of $700.
Security deposit is set at $500.
Guest thought that when they left, they'd get $500 back and the total trip was $200.
Just let them know that the security deposit was never charged.