The bottom part of the Glass Panes is z-fighting with the top part of the cobblestone half slabs placed as a top half slab, as shown in the picture (far right) below. That picture is depicting the slabs are top half slabs, by comparing the positions with a regular block, being depicted while it is being punched. The cracking has nothing to do with the glass pane z-fighting issue.

How to reproduce:

1. Put a half-slab down, making it a top half slab.
2. Put a glass pane on top of it.
3. Notice the bottom of the glass pane z-fights with the top half slab.