VLC is set to stream all elementary streams (--sout-all) by default. It is quite confusing for ordinary users using Converting wizard (Media > Convert/Save...). Try to use Streaming wizard (Media > Stream...) which contains check box for this option (:no-sout-all) in the last step there. Then use :sub-track option to select a desired subtitle track. You can use these options in simpler Converting wizard, too:
https://forum.videolan.org/viewtopic.ph ... 89#p484379