Chu Mu Yen won the men's under 58kg category and his compatriot Chen Shih Hsin took the women's under 49kg division but the standard of refereeing was the main talking point on Thursday.
Taekwondo contests are run much like boxing, a central referee keeps order while three corner judges keep score and two from three need to agree for a point to be awarded.
On Thursday, many competitors and their coaches said they got it all horribly wrong with three contests involving Egyptian men's bronze medallist Tamer Bayoumi attracting complaints.
Before that, though, Thailand's Yaowapa Boorapolchai looked to be robbed of a place in the semi-final after the judges missed a clear kick to her Cuban opponent Yanellis Labrada's head and another body kick.
Yaowapa's Korean-born coach Choi Young-seok refused to leave the arena, holding up the next bout, and a subsequent appeal was rejected by World Taekwondo Association (WTA) officials.
"What you saw was that Yaowapa kicked to the head once and the body at least once but the scores did not come up," Thai team chief Primal Srivikorn said. "We are angry and upset ..."
Greek Michalis Mouroutsos took on Bayoumi at the quarter-final stage of the men's under 58kg class.
"The referees didn't give me one or two points that I deserved and on the contrary they gave my opponent three points that came out of nowhere," said the local hopeful after his 8-2 defeat.
Another coach enraged by the standard of refereeing was Osualdo Garcia Delacruz, whose charge Gabriel Mercedes of Dominican Republic was beaten by Bayoumi in the repechage.
A succession of successful kicks from Mercedes failed to receive their just rewards even though he drew blood with a viper-like strike to Bayoumi's face.
Furious, Garcia Delacruz threw in the towel seconds from the end of the 5-0 beating.
Mercedes was duly eliminated but the frustrated fighter was treated to a standing ovation as he left the arena, while the four officials were berated by the crowd.
Bayoumi was involved in controversy for the third time, and booed off the mat after winning a bad-tempered bronze medal decider against Spain's Juan Ramos.
Ramos was docked three points for a variety of infringements after he became increasingly frustrated by the scoring and lost 7-1.
World champion Chu was the class competitor in the men's field, combining dazzling foot speed with high-kicking combinations to bamboozle his opponents.
In the final he was simply too good for Mexico's surprise package Oscar Salazar and a dynamic second round enabled Chu to open up a 4-1 lead, which he extended to win 5-1.
Chen piled final heartbreak on Cuba's world championships silver medallist Labrada, edging a close final 5-4.
Yaowapa got a small measure of compensation for her earlier disappointment when she won the women's bronze by a narrow 2-1 margin against Colombia's Gladys Mora.