Well, you seem to be doing the right stuff. Certainly Arabic script with its variant median and ending style characters is challenging.
Try a different font.
There are a problems with Books formerly called iBooks and Apple. I ignore it by using Smashwords to redistribute my epub2 to Apple.
Years ago the docx uploads to Amazon KDP lost chapter page breaks and Amazon support told me to upload the same epub2 to KDP as I used for Smashwords after they got a copy and verified it was converting to mobi, azw3 and KFX fine.
So now I upload the same epub2 to Amazon, Smashwords (who redistribute to Kobo, Apple, Barnes & Noble etc) and Google Playstore Playbooks.
The Arabic won't work at all on the four old mobi only Kindles, K1, K2, DX and DXG. The K3, Touch etc all need FW upgrades for azw3 so Arabic works.
The 3.4.3 or later for Arabic
https://www.amazon.com/gp/help/custo...MQC26VQQMM8XSW
Try disabling "Look & Feel > Fonts > Keep ligatures" as that's probably for Latin-Roman etc such as æ Æ fi œ Œ etc.
Try a different Arabic font. Find an ebook (azw3 or epub2) that has embedded font that works OK and use Calibre Editor to see what font it is.
I also test any new fonts / CSS style/format ebooks created in LO Writer (only edited in odt and extra save as docx for Calibre) on physical eink Kindles (Mobi only till recently, and azw3, sometimes check after publish Amazon azw3 & KFX download as the is no longer any real preview) and variety of brands of eink epub readers (Sony, Kobo, others) from 4.7" to 10.3", and Android Apps on phone (4.3" to 6"), tablet and eink.