I have version 1.4.1 of Noxys Waterfill installed along with version 1.13.1 of the Miniloader mod by Therax. I found an issue whereby if you were to place waterfill underneath of a placed miniloader instead of removing the miniloader and returning it to the player inventory like other entities, the miniloader entity seems to be deleted while leaving behind the sprite of the miniloader floating on the water layer. If landfilled, the sprite remains on top of the landfill. This sprite remains even if I try to overwrite it with a larger entity such as an assembling machine, however I am unable to place transport belt in the same tile as the miniloader sprite. It can't be destroyed by explosives and construction robots make an attempt to remove it if scheduled for demolition, but end up failing to remove the sprite. The sprite remains even if the game is saved and then re-loaded, and the editor tools aren't able to remove it either.

Unfortunately I can't do anything about this from my end afaik. I'm not sure if Therax can either since "destruction" by waterfill is not really a known "event" and it is already surprising to me that other entities get returned to the player inventory. Are you sure they are returned to you?

Either way I can't do much here as Therax's mod will have to handle their entity destruction since they use hidden entities (which is the reason you can't place belt there).

I've now resolved this issue (in version 0.4.2) on my and by no longer allowing waterfill to be place able over entities. This fixes among other things accidental deaths, cheasily deleting biters and their nests, issues with mods that need to handle destruction or removal in a special way like the miniloader.