ffmpeg doesn't merge streams. You specified two input files, so ffmpeg took the first audio track from the audio file and the first video track from the video file. In order to merge two audio tracks you should use some audio editor, like audacity.
If you want the output file to have two audio tracks, use `-map` option, that'll look something like this:
-map 0:0 -map 1:0 -map 1:1
That'll tell ffmpeg to use the first stream from the first input file and the first two streams from the second input file. Otherwise by default ffmpeg uses one video and one audio track.