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.
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We're tracking this issue in MC-127237, so this ticket is being resolved and linked as a duplicate.
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Waterlogging a block affects the entire airspace on both sides. It is not possible to 'half-waterlog' a block.