Judging from the tone of the tweets that have been sent to Joe, along with the number of threads that this problem consumes on the Windows Phone website, this is a hot-button issue that is affecting a lot of users. One app that seems to help, if you believe user's comments, is called Shrink Storage which is available from the Windows Phone Store. A few users said they were able to re-claim 1GB of space and more. It's a free download and is designed to fix the "other" storage issue.
source: @joebelfiore, WindowsPhoneDaily, WindowsPhoneStore via WMPoweruser
Belfiore's tweet says a fix is coming