This is using modifications to the Minecraft Server itself, but the bug lies on the client-side so I hope this issue isn't ignored because of that.
It's easily displayed in the attached picture, but when a map is rendered with transparent pixels, glass and entity heads behind the map do not render. Other items may not render as well, but these are the most apparent ones. The Resource Pack being used removes the texture for the back of an Item Frame allowing for transparent map images.
This hasn't been able to be tested in 1.9 Snapshots due to the modifications to the Minecraft Server not allowing snapshot connections, however it can be assumed the bug is carried over into newer versions. Thanks!

Update: This appears to still be an issue in MC 1.10.2 and the latest snapshot 16w42a. After some testing, I've found that regular clear glass panes are visible behind maps, but colored glass is not. 1.10.2 was tested in the screenshot 2016-10-21_16.54.54.png and 16w42a was tested in 2016-10-21_17.00.46.png. Also, 2016-10-21_17.00.59.png showed what was behind the map for reference.