Let's consider the following scenario:
You want to split a gif in individual frames, that can be done nicely with image magick with the following code
convert canvas_prev.gif -scene 1 +adjoin frame_%03d.gif
Then you want to copy another image over each resulting frame
composite -gravity center frame_001.gif new.gif composed_frame.gif
And here's the catch. When you copy the frame over the new image image magick the transparency around the image frame gets clipped and the positioning will be different.