Well it's certainly weird and I have no idea why it's happening in RTL, but if we fix a similar bug in LTR, this gets fixed too.
In LTR, when a link appears at the end of a line and wraps onto the next line, the popup might appear below the words on line one or below the words on line two. Because the carriage return will place the words on the next line on the other side of the screen, this means that the pop-up can appear on the opposite side from where the user is hovering. If we apply a rule to popupable links not to apply word-wrapping to the contents, then we avoid this problem and the strange behavior you see doesn't happen.
This will be fixed in the next build. I am working on it now.