Mine is still there. It seems more transparant now, and is lower on the right side of the screen than it used to be. Maybe it got disabled?
Settings | Advanced features | S Pen
Show Floating Icon (on is to the right)
I may be misunderstanding... The S Pen bubble is supposed to only be there when the S Pen is not in it's "garage", it cannot be tapped using anyting other that an S Pen, so this is the intended functionality.
This was likely a bug, it was likely not being detected as being in the holder or garage. What you are seeing now is the way it was intended, and shows that things are working properly now, unless that floating icon is not what you are referring to...