Swarm of rats, half-decomposed/eaten corpses. Body parts.

This is the Delayed Drawn symbols that strikes. This features reapplies symbols after the effect pass to handle certain visual problems, but it only applies to non-building symbols (And with building symbols, I really mean symbols with built-in roof shading, like that tree also has)

Might be better to separate those into different sheets, but you can also fix it by disabling delayed drawn symbols, juts type DELAYDRAWSYM (enter) on the command line, and answer the prompt with 0 for disabled.

Note that this lasts the current CC3+ session, it is not a per-map setting.

Effects cannot be trimmed. You'll need to cover it up with something.

Personally, to prevent things from extending through a wall and into the "nothingness" behind, I like to use a mask that is made up from the background with holes punched in it for the dungeon (using a multipoly for that) and put that on top so it basically covers up everything outside the walls, including unnatural shadows.

Notice that this behavior can indeed be automatic with the drawing tool, and it is that behaviour the instructions was written against, but it seems that most drawing tools doesn't use it. But if you edit a drawing tool, you'll see it has a setting labeled attach mode, which can be current settings, on or off. Current setting refers to the global attach option, the button down in the lower right of the main gui. On or off is just forcing it to be always on or off. Right click the attach button in the lower right to select exactly which attach option to use, I think endpoint is the default. (The drawing tool can unfortunately not specify which attach option to use, only if it should be used or not)