Edit: I've just tried rendering the video as AVI using after effects and not adobe media encoder and the problem was fixed but the file is too large (because of obvious reasons) so It would be hard for me to upload it to Youtube.
No issue there. Nothing stops you from giving it an extra encoding pass in AME to produce a lean H.264 file. Ultimately that's what you need to understand - working with intermediate files is a common practice amongst professionals for any number of reasons. Otherwise the issues you are seeing are just bugs and limitations in current versions of AE combined with teh fact that AE is not an audio editing and mixing app in the first place.
Professional, and that means effective and economical, video production workflow.
- Script and plan your story as carefully as you can
- Shoot the highest quality shots and performance you can get in a reasonable amount of time with the equipment and staff you can afford
- Capture the best sound you can on location using the best equipment and staff you can afford
- Copy all of the original footage and audio to at least two backups on different media to protect your work (Adobe Prelude)
- If you shoot highly compressed footage or have a lot of footage you should go through the footage and index the best shots so you can reduce the amount of footage that you need to transcode to a DI (digital intermediate or mezzanine codec) for production
- Rough cut your project using a good NLE including audio, video and place holder graphics if needed (Adobe Premiere Pro)
- DO NOT try to cut long projects in a single sequence or timeline - break the rough cut up into scenes or acts
- In the fine tuning process of editing your project select the shots that need visual effects or other special processing and separate them out for further processing
- When you process your shots or short sequences that need extra work in an app like AE work on only the portion of the shot that needs the work, do not waste time with a five minute take when you are only going to need 7 seconds of the shot in the final edit (Adobe After Effects)
- Fine tune the audio and video edit in your NLE using rendered effects shots for anything that is complicated so the story works and the edit is approved
- Move all your audio to a good sound editing for final processing and mixing (Adobe Audition)
- Return to your NLE or compatible color grading software to do final color grading (Adobe Speed Grade)
- Render an archival Production Master to a suitable visually lossless frame based codec
- Render your deliverables using a suitable compression application (Adobe Media Encoder)
- BACK UP everything with a well managed redundant system instead of a bunch of single external disks (Here's a webinar)
Even on short projects like 30 second TV spots I almost always use this entire workflow. You open more apps but you get a better product in less time when you use the right tools in the right order.
Editing a 15 minute video in After Effects is usually not the best use of the software. 90% of my AE comps are 7 to 10 seconds long and the editing is done in Premiere Pro. It takes a little better organizational and planning skills but it is way more efficient.