What kind of paragraph composer are you using?
Maybe there is a bug in the "Global Paragraph Composer"?
Can you make a snippet file (idms) available for downloading (via Dropbox or something like that) a sample?
Did you use shift+return? (Forced Line Break) Avoid it.
More information we would have, if you included a screenshot with non printing characters turned on.
Would you encounter the same problem, if you choose a different font As far as I see, you have also problems with missing characters like é or è or ê. So you will need a more complete font anyway.
1. I don’t have the used font, so I used Minion Pro Regular instead.
2. Your story is set to RTL, I changed it here to LTR text.
With this 2 changes the problem is not existent here. I suuppose that this is a font problem.
But you should also create Paragraph Styles and use the correct language, both is not done.
Thank you for providing the sample IDML file.
I still think it could be the used paragraph composer, maybe in conjunction with the used font. I'd change the composer to see, if the problem will go away.
@Willi – you are right, the story direction is RTL, but the paragraph direction is LTR. That's no surprise here since the ME version of InDesign was used.
I would change story direction to LTR, use the "normal" paragraph composer instead the global one.
Since the used font is not available to me, a substituted font is not showing the problem.
But that may mean nothing. I do not use the ME version of InDesign…