A quick google search comes up this these:
Based on those solutions, may be you can add
\DeclareUnicodeCharacter{200b}{}
I haven't tried it, so cannot guarantee if that will work.
I regularly generate pdfs and almost all of my org documents would be using 0x200b somewhere. If a pdf generates fine without any visible artifacts and with all content as expected, I do not look into the tex compilation logs.
This time I checked the log and I don't get that error, but a warning instead. Note that I also use XeTeX which has unicode support. Below is a snippet from my log:
This is XeTeX, Version 3.14159265-2.6-0.99991 (TeX Live 2014) (preloaded format=xelatex)
\write18 enabled.
entering extended mode
(/home/kmodi/sandbox/org/italic_quotes.tex
LaTeX2e <2014/05/01>
Babel <3.9k> and hyphenation patterns for 2 languages loaded.
(/home/kmodi/texlive/2014/texmf-dist/tex/latex/base/article.cls
Document Class: article 2007/10/19 v1.4h Standard LaTeX document class
(/home/kmodi/texlive/2014/texmf-dist/tex/latex/base/size11.clo))
(/home/kmodi/texlive/2014/texmf-dist/tex/latex/base/inputenc.sty
Package inputenc Warning: inputenc package ignored with utf8 based engines.