This is intended, as Broken Shards can be used for Crafting, as well as for creating Runes. As an aside the Knowledge Point Bar is only intended to hold 10-20 Knowledge Points (depending on whether an Inspiring Meditation is cast) and to also offer a temporary space when winning Knowledge Points. Its design was not to create a permanent holding space, as this means 24 Knowledge Points a day are missed.  

There will indeed, when this gets to the live server. But as this is Beta only currently, its not really relevant.  

The information was released last year, for anyone that perhaps missed it, here it is.