Not going deep enough wouldn't cause an infection, but it would cause redness and most likely inflammation. Quads, butt cheeks should be done at 1.5'' depth, with delts around 5/8 - 1'' depth.
I am on trt and have been doing sub q shots lately. I shot 0.1 ml into area around my belly button, it's now a small knot, slightly red, slight tender to touch. I am sure the redness is irritation and not infection
Like you i always swab vial with alcohol, clean area thoroughly, etc...
I personally have done .5 ml of masteron prop with no issue into quads, even when i was going too shallow. Once i went up to 1 ml, using same technique the area got red and was damn sore.