This happens with animated images. Specifically with your example screenshots, they are the different states of a button (idle, selected, hovered) and buttons in Siglus are typically doubled up on cuts. Basically there are duplicate frames. For Angel Beats! I believe the frames were something like Image 1 > Image 1 > Image 2 > Image 2
How to deal with them depends exactly on what you want to do. For extracting them, the best solution would vaconv.
Putting them back together could be done in multiple ways. The quickest method would be to use the same regions presented in the accompanying text file, but you could also manually add the additional cuts into the g00.
Edit: I quickly drafted up an example using one of the images you screenshotted.
Extracting the image with vaconv:
vaconv __sys_bk_chk00.g00
Gives us the image and the text file.
Recompiling:
vaconv __sys_bk_chk00.png -g2
Gives us the final g00.
