When i have added items to the layout, and have teh grid on it may appear all aligned correct.
I then press cntl, and drag to make a copy object and change its size, it still appears fine.
however when i now move this object it jumps to between the grid lines.
Hard to give an exact example as i have copies of copies but playing around with making an object from size 100, 600, then clone it and make it 25,600 on a 25 grid and it does off grid.
origins are all correctly aligned.
A good test actually, make a 25 , 25 grid.
then make a sprite, resize it to 25,25, check origin is 12.5 and fill it black. on the layout it now sites between your grid of 25 lines.