In the .opf file there many different language data entries. One of them is Arabic, which is a RTL language.
Code:
<dc:contributor opf:role="bkp">calibre (2.78.0) [https://calibre-ebook.com]</dc:contributor>
<dc:language>ar</dc:language>
<dc:language>de</dc:language>
<dc:language>en</dc:language>
<dc:language>fr</dc:language>
<dc:language>it</dc:language>
Many reading system will only use the first dc language metadata entry = Arabic.
You might want to get rid of all non-English dc language entries.
Code:
<dc:contributor opf:role="bkp">calibre (2.78.0) [https://calibre-ebook.com]</dc:contributor>
<dc:language>en</dc:language>
Also note that the Guide section in the .opf file contains the Arabic word for TOC:
Code:
<reference type="toc" title="المحتويات" href="Text/toc.xhtml#calibre_generated_inline_toc"/>