tattoos don’t bother me, since I know they only stay on the surface. Shallow needles are ok. They’re painful though!
What I hate is the deep, lingering Novocaine needles at the dentist, and having my blood drawn. There’s something about the violation of the inside / outside separation that fundamentally scares me.
There’s a recurring trope in the MMF/m sizey scifi novel that I wrote that plays with this fear. The main character constantly crosses this boundary.