Disabling Command + Arrow scrolling
If your intention is to globally override this behaviour, this will do the trick:

Create a file called DefaultKeyBinding.dict and write on it the following:

    {
      "@\UF700" = "noop:";
      "@\UF701" = "noop:";
    }


@\UF700 is the Unicode value for Command+Up while
@\UF701 is for Command+Down.

Save it and place it under ~/Library/KeyBindings/. If the folder doesn't exist, just create it.

A different approach would be to override this shortcuts on each of the Applications you're having troubles with, assigning the problematic shortcuts to the Application's function you usually don't use, for instance.