I suspect you've built your facility on a magma pipe 48*48 mid level tile. In those tiles new magma is generated at the magma pool top level or the highest level with direct downwards "visibility" of SMR (whichever is lower), and my experience causes me to suspect this "rain" can occasionally flow sideways to fall on surrounding tiles without SMR visibility. This "rain" stops when the top level is 7/7 at the magma pool top level, and resumes when the pool is drained (or when you expose air at a lower level to the SMR).
If my guess is correct, I'd recommend building a floor over the hole and make another one outside of that mid level tile, Furthermore, I'd recommend not having a hole directly down to the magma sea, as critters can get out from it if you do.
Instead, I typically dig a tunnel at the level of the top of the magma sea horizontally up to, but not through, the sea. I'd then clear out a workshop area on the level above with holes down to this tunnel for each workshop, a magma safe drawbridge airlock at the end of the tunnel (by the sea), and when done (and the drawbridge levers have been tested), channel away the last tile between the tunnel and the sea from above, causing the magma to flow into the tunnel. Immediately build a wall or floor to block the breach caused on the workshop level. Once the tunnel is full of magma (or at least has at least 5/7 magma in it), close the airlock to secure the workshop area from incursions from below. Note that the holes in the roof of the tunnel cannot rain magma, because the bottom of the tunnel is ordinary rock, not the SMR.