That is so wrong.
Application for the Non Imm O Visa requires the money to be in the bank on the day of application.
From then on the requirement is money in the bank for 2 months on every 12 month extension application.
As her application at Phuket immigration was accepted it seems a bit strange that it got turned down at head office without reason.
The fact that Phuket accepted it means that it must have complied.