Answer:

It is hard to make sure Beep works with all sites 100% correctly because developers use thousands of different tools to create their websites. This may lead to the comments you create showing up a few pixels off, or, in very rare cases, seriously misplaced.

Despite that, our mission is to make sure all comments are displayed correctly 100% of times, so we are currently working on all of the issues.

What may work is to delete the misplaced Beep (copying the message beforehand) and then creating a new Beep a few pixels away from the original (pasting the copied message into the comment box).