@Leena **********
if your Thai Citizen Children made Entry into Thailand using their Australian Passports, then they must use their Australian Passports to Exit out of Thailand (and, for many purposes, including Thai Immigration purposes, still considered Foreigners inside Thailand using Australian Passports and still subject to Thai Immigration Fines, even if they are Thai Citizens at Birth)
There are several options available to your Dual Australian Citizen + Thai Citizen Children:
1.) the easiest and most straightforward method without any travel outside of Thailand is to obtain Thai Ancestry/Thai Descent ( เดิมคนไทย ) 1 Year Extensions of Stay at your local Thai Immigration Office; if staying in Bangkok, you can go to either the IT Square at Lak Si or Chaeng Wattana ( ตม.1 ); otherwise your relevant local Provincial Thai Immigration Office
2.) FLY out of Thailand (using the same Australian Passports they initially made entry with) and then Make Entry Again into Thailand using their Thai Passports BEFORE their initial stay EXPIRES
3.) Nowadays, your Thai Citizen Children could overstay on their Australian Passports, and, if the Full Names on Both Australian + Thai Passports are the same names (matching full names), then they will be waived overstay fines as Thai Citizens using Foreign Passports, and, also the old, Rescinded Thai Immigration Policy Penalty for Thai Citizens using Foreign Passports