Any hours outside of the families booked hours should be charged as unbooked hours on your timesheets NEVER cash in hand.
So if you have 6:30-3:30 and they arrive at 4:30 then you charge from 3:30-4:30 unbooked hours rate on the timesheet. What timesheet system are you using?
Timesheets shouldn't be done till towards the end of your pay week/ fortnight to allow for these extra hours. If it is the last day of the pay week/fortnight they can wait a bit till you fix it up once they arrive or get them to text you when they are leaving work so you know what time and can fix it before they arrive or if your scheme doesn't mind it being submitted unsigned you can do it and get them to sign it the following week.
Don't short change yourself, we are paid little enough as it is in childcare to be doing extra time without pay, and a lot of the time it is only one child you have at that time of day so you are really working for nothing much.
What your scheme said is true, you should change their booked hours if it is happening on a regular basis, it doesn't matter if sometimes they don't use it it just saves you all this mucking around and they know what they are up for each week without it changing from week to week.
I also don't have a late penalty fee but I do let my families know if they start to get slack that I can implement one if they take advantage.