Been running into an issue when rendering from After Effects to Media Encoder since updating to 2015.3. When sending an AE project to AME, it will render a portion of the audio at the end of the video even if there is no audio. I have tested rendering in AAC, Dolby, and MPEG audio codecs in AME and the issue persists. I then used Premiere to import the AE project and could see on the waveform that during the import process out of AE, the audio is repeated. When rendering out of AE for an intermediate format, there is no audio loop. It appears that this issue is only coming up when trying to go from AE and render in any other Adobe software.
I've also found that people have been having this issue and others similar for over a year at this point. Adobe even closed one forum that had this issue open, and marked it as answered, which it clearly has not been.
Original Thread: Rendered Audio Repeat Glitch
Reddit Thread (Similar issue): https://www.reddit.com/r/premiere/comments/4l76tz/has_adobe_really_not_fixed_the_audio_loo ping_at/
Video Rendered through AME with Youtube 1080p HD preset
This is a bug. There have been a number of threads about this. The AE and AME teams are aware of it and are working on a fix. (There is a thread where they go into extreme detail about the cause of the bug, but I don't recall the link at this time.)
The easiest workaround is to make your comp a few seconds longer (with an audio layer for the entire duration) and then trim your work area to where you actually want the video to end.
This issue is fixed in the After Effects CC 2015.3 (13.8.1) bug-fix update. This update, available now, can be installed using the Creative Cloud desktop application, or by choosing Help > Updates inside any Adobe application.