With your code as it is, it's overwriting the default masks of some entity types with what you have set as a default. You can see the default masks in the \Factorio\data\core\lualib\collision-mask-util.lua file. While many are what you are using, some are not.

I suggest adding this to the top of your file:

local collision_mask_util = require("collision-mask-util")

And then changing these lines (145-151):

if prototype.collision_mask then
    table.insert (prototype.collision_mask, "resource-layer")
    log ('added: ["' .. prototype_type_name .. '"]["' .. prototype_name .. '"]: ' .. serpent.line (prototype.collision_mask))
else
    -- prototype.collision_mask = {"item-layer", "object-layer", "player-layer", "water-tile"} -- default
    prototype.collision_mask = {"item-layer", "object-layer", "player-layer", "water-tile", "resource-layer"} -- one more
end

To this:

local collisions = collision_mask_util.get_mask(prototype)
collision_mask_util.add_layer(collisions, "resource-layer")
prototype.collision_mask = collisions
log ('added: ["' .. prototype_type_name .. '"]["' .. prototype_name .. '"]: ' .. serpent.line (prototype.collision_mask))

This allows the code (via .get_mask) to pull the current mask or appropriate default if nil, then .add_layer makes sure that it is only present once (in case another mod already added the "resource-layer" to one or more entities), and then finally you're setting the new mask table back to the prototype.

Can you please apply this changings?

I can, sure. Gimme a few to apply them and make sure I didn't typo anything (:P), then I'll upload it.

By the way, I'm seeing some old code in here that's been commented out that appears to be related to a setting that's been commented out as well. Did you want all of that left in there, or is it ok if I clean that out?

Yes, it was here to be sure that I can go back to the working code :)

Ok, I left all of that alone, then.

Uploaded 1.2.12, with updated code in data-final-fixes.lua, updated info.json for version number, and added entry into changelog.txt.

@FuryoftheStars
Thanks, man!