https://github.com/pixelwhipped/ModMash/pull/11
Basically, you were not letting other mods know when you destroyed their entities.
Also, something is wrong with how you create and scale icons. I tried finding the problem, but gave up. Here's a screenshot of what it looks like (in an infinity chest -- the only place I see the problem, but still really annoying) https://i.imgur.com/aB8aYkI.png
And here's what factorio-current.log has to say about it:
4.923 Warning AtlasSystem.cpp:155: Image "base/graphics/icons/artillery-targeting-remote.png" was used for an icon multiple times with different scale. Icon background might not be consistent with other icons.
4.930 Warning AtlasSystem.cpp:155: Image "base/graphics/icons/artillery-targeting-remote.png" was used for an icon multiple times with different scale. Icon background might not be consistent with other icons.