I’m trying to make a model of a cartoon character (Invader Zim) from scratch. The arms and legs are made out of cylinders and cones, but when i try to join them to the rest of the mesh, some of the parts turn inside out! 
It seems to only happen with the cylinder and cone shapes. I don’t know how to fix this can somebody help me out here? I’m familiar with some things in Blender, but i can’t seem to find anything to help with this problem. I’m attaching the Blend file so you can help and find out what i did wrong. (i’m kinda new to blender, I’ve played around with it for a long time, but this is my first model I’ve tried to put a lot of effort into)
Attachments
Invader Zim Blender project1.blend (1.15 MB)