Carcel and Yap failed to impress the judges in their matches as they succumbed to their opponents from Pasig and Laguna, respectively.
Coach Kenn Toledo cited the "unfair officiating" as the one of the main reasons why they lost in their games.
"I know the rules and regulations in taekwondo very well. Most of referees were new and inexperienced," Toledo said.
The eight year-old Carcel is one of the most promising jins in this year's Milo Little Olympics and have won her last five tournaments before to the MYG.
Yap, son of well-known former RP team member-turned coach Danny Yap, was a silver medallist in the prestigious Samsung Best of the Best Taekwondo Championships also in Manila a few months back.