The Drag & Drop from items in the inventorys only works if you don't release the mouse button, and pull over the item to the slot. If you just click on it and move the cursor, the item do not get selected.
Environment
Fedora 23 (x86_64); Fedora Rawhide/24 (x86_64) all other distributions using Wayland
GNOME Shell 3.18.0+
xorg-x11-server-Xwayland 1.18.0
Is this still an issue in the most recent versions (currently that is 1.10.2, or 16w42a) of Minecraft? If so, please update the affected versions and help us keeping this ticket updated from time to time. If you are the owner/reporter of this ticket, you can modify the affected version(s) yourself.