How to Align Footnote Reference Numbers to the Right in Arabic Text in InDesign?

Not entirely sure - I don't often use the ME version of InDesign

However, here's what I think is going on and how to fix it: 

In a Middle Eastern version of InDesign, footnote reference numbers are usually inserted as part of the main text. That means they inherit the default text direction, which in Arabic makes them show up on the left. To get them to align to the right without messing up your Arabic text, you probably need to create a custom character style for those reference numbers.

Try this:

Open your document and create a new character style specifically for footnote references.
In the style settings, check the Bidi Options (or the section where you can set text direction) and choose right-to-left.

Now go to Type > Document Footnote Options. In the Formatting group, assign your new character style to the Footnote Reference Number.

Make sure your paragraph settings for the Arabic text remain untouched so that only the footnote numbers get the RTL treatment.

This might force the reference numbers to behave like Arabic text while leaving the rest of your layout intact. If it still gives you grief, double-check the overall text direction and any indents or tab settings that might be influencing the numbers.

If that's not working let us know.

- Probably could do with a Text File and then I could download the ME version and see if I can get it to work for you.