Having this this issue since few versions now.
some files dont play the audio very well and sometimes the subtitles disappaer.
anyone else?
Is your Apple TV connected to an AV receiver or just a TV? If just a TV, you may try disabling the AC3 and DTS audio options found in the Media > Settings > Playback menu.
Regarding subtitles, you may try adjusting the encoding type as described here.
thanks! 
apple tv is connected with hdmi to my tv. used to work with ac3 and dts audio enabled, but as long i dont use it… i can enabled it.
subtitles i have to test