I see - it seemed like being able to use the Factoriopedia while the game was paused was an intentional decision. But in that case, I guess the bug would be that the Factoriopedia, tech tree screen, and tips and tricks window are still interactable when the game is paused, and that they all draw ...

When the game is manually paused with the pause keyboard shortcut, keyboard shortcuts ignore windows that are still interactable, behaving as they would normally if the windows were not open.

The best example that I have that demonstrates why this should be considered a bug is with the tech tree ...

It seems to me that you could just filter the cargo wagon slots: