If you have correct settings on your sequence in Premiere and in Media encoder, this should not happened.
If you import a 4:3 file directly to Media encoder and get this problem, create a Premiere project and a sequence in the correct resolution and aspect ratio, and import the file and drop it on the timeline. Save and quit premiere, and import the Premiere sequence into media encoder. Now the aspect ratio should be correct. Premiere should read the aspect ratio correctly, and Media encoder should read the sequence from the Premeiere project correctly, and there should be no more problem regarding aspect ratio.
The problem for me was when trying to import the file directly to Media Encoder. Make a Premiere-roundtrip as explained above, and it should work just fine.
Don't forget that AME has an Interpret Footage feature (similiar to Premiere) that allows you to change the pixel aspect ratio of your source files. Just select the file in AME's Queue and choose File > Interpret Footage. From there you can change the PAR, frame rate, or field order of your files before encoding them.