medyo magulo pero this can be easily handwaved.
let's start sa part where the yangdonese characters were in the philippines.
1. jao and anand were shown to have learned filipino beforehand (from gino and isabel respectively), so they are shown as being able to converse easily with the filipino characters.
2. behati is shown to be a highly intelligent woman, so she could have learned the language rather quickly. notice at the start na nakikpag-usap siya kay mikay in english, but as her stay progresses, unti unti siyang nagsishift into talking to her in taglish then fluent (but still accented) tagalog.
3. dorji and han are implied to have stayed in the philippines for a long period so they could have already learned the language beforehand.
now let's move to the yangdon scenes. this can be interpreted as the characters already speaking in yangdonese (translated to tagalog for audience convenience).
1. mikay had learned basic yangdonese from her early trip at the start of the series. she then learned the language more completely while working as jao's, and then behati's, personal assistant. also nag-aral pa siya ng karagdagan nung nalaman niyang prinsesa siya. but at times, she prefers speaking in tagalog when conversing with yangdonese characters who understand it, like anand, jao, and behati.
2. gino is already a yangdonese speaker, owing from his one or two year stay in the country during his childhood. notice na dun sa scenes which were shot in bhutan, he converses with actual bhutanese characters in english. this can be seen as him preferring to use english while he is still learning the language more.
3. vicky is still learning the language, kaya she prefers to speak in tagalog when talking to mikay or the other characters who understand filipino.
sinubukan na nila nun yung dub method nun in the early episodes, but it was heavily criticized. writing an entire script or scripts in bhutanese (for the subtitle method) would be a logistic headache for the writers since hindi naman sila native speakers (remember na lengthy series ito). out of the question na yung paggamit ng fake bhutanese, as the writers are probably already aware na madaling mapapansin audience yung fakery.
note na hindi to sign of laziness on the writers' part. the method of letting the actors speak in their native language while implying that the character is speaking in a foreign language is a common method in tv production (alam ko ginamit rin to sa heroes dun sa edo arc nila).