Okay, there are probably a couple of things going on here.
First, when I try this, I do not see any problems. I tried with two fonts in English and all the fonts that support Hebrew on my machine. Regardless of whether I have Fractional Widths or System Layout, I don't see a problem. This screenshot is with System Layout selected. And, please note, the default is actual Fractional Widths.
Have you checked your Indent settings in your Paragraph panel? How about resetting both of these panels? You can do that in both the Character panel and Paragraph panel flyout menu.
Assuming that's not the problem, this might be the font you're using. Which one is it?