As said in the title if you place a water source on a block that has a glass pane, the water will go through the glass pane.

In the first image you can see the example of a simple construction I've made in creative for the sole purpose of this bug report.

The second image has been taken after placing a water source on the grass block but effectively at the same block that contains a glass pane.

The third image is the other side of the glass pane showing that the water does indeed go through it.

I would've expected the water to only take half of the glass pane that it's been placed on kind of like when you put water in a staircase or when you have to fill the airgaps by placing a water source on top of an underwater slab.