Rendering through After Effects is Buggy

There are tutorials on Rendering in the User Guide. Please spend some time there. 

Until you have a good understanding of video standards, formats, and compression technology it is usually a bad idea to open up the Output Module or Media Encoder render settings and start messing with the switches. It is even a bad idea to choose custom composition settings in After Effects or custom Sequence settings in Premiere Pro. You should not be using MP3 as a video source file. The standard for sharing is now an H.264 compressed MP4. The Media encoder has different presets for all of the standard delivery systems and frame sizes. I would start by choosing the YouTube HD or Vimeo HD presets you find in the H.264 presets section.

You have to choose the codec AND container you want, these are not automatic choices and I doubt anything is broken, you just need to figure out what your output settings are.

MOV is a container, but this only tells you part of the story about your file. Think of it as a box with features, but the box  itself has nothing to do with the contents inside. 

A Codec is the algorithm used to compress your video which then gets "wrapped" inside your desired container. For example, Animation, ProRes, Cineform, DV, and DVCPro HD are all codecs that can be wrapped in a MOV container. Those last two won't play in the current version of QuickTime anymore because they're old, 32-bit codecs. Apple deprecated these old codecs so only modern formats are supported. QuickTime X is not a good way to look at your media because if your file even plays but it's not a desired codec, QuickTime will actually convert the file again (depending on what version of macOS you're running). It's very happy with ProRes and H.264 files, though.

The fact that you can import back into AE is a good thing. At the top of the Project panel, with the File selected, please post a screenshot of the info there. You'll see the Codec information and file specs. Even better, though, what are the Output Module settings you're choosing in After Effects? Screenshots are good here too.

As for the MP3 being created out of Media Encoder, that's because MP3 was likely the last format you chose when using AME previously. Again, you have to specify what you want your settings to be, and there are a lot of settings to deal with.

So in short, I doubt anything is buggy here, you just need to pick the correct settings. Correct settings depend on what you want to do with a file. Is this to be used in editing or for final delivery? If it's going to be dropped in a sequence that's being edited, then you want an intermediate file with little compression like ProRes. If it's for final delivery then H.264 is a good format. AE doesn't export H.264 directly, but you can queue your sequence back to AME, choose H.264 as the Format, then choose a high quality preset like one of the YouTube or Adaptive presets.

also a quick note - rendering through the adobe media encoder seems to have worked well.  the difference being the codec, the AME produced a .mp3 file with some compression applied. interesting.