I fairly certain it is this mod causing the bug, I am playing krastorio 2 and space ex together, however when I load those without this mod, landfill works?

Same issue with Nullius, can only landfill "shallow" watertiles which are slowly walkable, not the normal/deep watertiles.
Krastorio, SpaceEx and Nullius all run with Alien Biomes.
1.1.60 experimental broke it, can use landfill when i remove Transport drones.

The bug is in data-final-fixes.lua, around line 77:
for k, prototype in pairs (collision_mask_util.collect_prototypes_with_layer("player-layer")) do

collect_prototypes_with_layer now returns tiles, too.

Fix: line right after:
if prototype.type ~= "gate" and prototype.type ~= "tile" then

Well don't have this issue on bob's alone it only appears when playing K2 SE in my case.

fixed it, thanks