You could try resetting Launchpad:
Read the entire article and be sure you understand the consequences before you do this.
Given how little Launchpad does and how simple it's supposed to be, it just doesn't seem to be worth the trouble for anyone other than a convert from iOS who hasn't yet learned Finder basics. My thought is: Drag Launchpad off your Dock and wait for a third-party developer to release a utility that allows Launchpad to be managed more easily (alphabetizing, group dragging, etc.), or for Apple to improve it. Or, just ignore it forever; you certainly don't need it.
I've had similar results and wasted a lot of time getting it just right only for it all to be back at a later date, it's buggy and not production ready IMHO
There's a freeware utility out there called LaunchPad Control that allows you to turn items off but you still have to re-arrange everything yoruself and it's also buggy and sometimes fails.
As John advised drag the think from your Dock and wait until Apple fix it or somebody writes a utility that makes it reasonable to use - your Desktop is not a touch sensitive iPhone screen and the two should never have been confused/merged in my view ...