1.0.0 Factorio, 1.0.4 Krastorio2. When I threw my creep-killing virus capsule, it removed all the creep, but left in its place an invisible entity that I can order my bots to remove with a deconstruction planner. They attempt to remove it, but pick nothing up, only clearing the red X. But the invisible entity remains, and can be ordered deconstructed again and again.

Probably u have other mods that make the script fail

Nope. K2 is the only mod I was using.

I just tested it in a new game with the same game and mod version (which are the newest) and I can confirm this bug. Here is a picture:

Using the Anti creep virus capsule does not delete the creep but changes it into those invisible entity that can not be removed. It ONLY affects already existing creep, newly generated biter nests are generated without creep or invisible entities.

These invisible entities are also causing the textures to glitch.

Same here. Factorio 1.0 with map 1.0, Mods: Krastorio 1.0.4 (new game), Alien biomes 0.5.8, Helmod 0.11.8