As far as I am aware, there is no way to pick up only a part of a stack of an item that is sitting on the ground at this time. If there is, someone feel free to correct me with how to do this.
I do believe the entire inventory system and the way things are handled with dropping and picking up objects are currently being overhauled, so this will most likely be fixed soon.
Until then, only suggestion I can make is try to be more careful and not carry more stuff than you can carry, if that makes sense.