In this case, it is caused by a combination of rules including the "one element per tile" mechanic. I am exploiting the rising property of Hydrogen (hydrogen generally can't move down except to fill an empty space or merge with another hydrogen packet). The specific combination of how hydrogen is allowed to move and the mutual exclusivity of elements in a tile results in an impossibility condition for the hydrogen packet.
In real world physics, the hydrogen packet has a path to escape, and if it were confined by an infinite well, it would end up engaging in quantum tunneling to escape. The sum total effect would be that it would spontaneously move from the confined location to the mass of hydrogen on the left as if it had taken a different path.
Besides a lack of a universal conservation of mass law in the game mechanics, the problems is the total confinement of the solid blocks. In real world physics, the solid blocks are actually in some sense porous even under the best of conditions; the conservation of mass and fundamental quantities as well as path of least resistance wins out over the confining ability of a physical boundary.
Solid block containers in Oxygen Not Included aren't leaky which results in these deletions. This machine demonstrates one particular case of gas deletion, but we can demonstrate this with doors and other machines, and it is presumable and likely provable that it happens "naturally" all the time due to similar conditions being reached by combinations of rules resulting in contradictory conditions that necessitate the mutual exclusivity of the mass of a packet on the one hand and the total impermeability of tile on the other hand.