I have not participated in an audit from an audit stand point but I recently attended a weeklong training on the FDA’s Quality System Regulation by AAMI University. The trainings were hosted by FDA, consultants, and at least half the class were FDA employees that were mandated to attend the course. It was a shared learning environment and the course instructors walked us through many example FDA warning letters. Interestingly, many of the 483s we reviewed were a result of companies not following their own procedures, not the lack of having established procedures.
These are a few of the top domestic observation according to 2016 DOC observations presented in training:

CAPA
(710 total)
21 CFR 820.100(a) # of observations 234; Percentage 33%
21 CFR 820.198(a) # of observations 201; Percentage 28%
21 CFR 820.90(a) # of observations 96; Percentage 14%

P&PC
(650 total)
21 CFR 820.50 # of observations 98; Percentage 15%
21 CFR 820.75(a) # of observations 84; Percentage 13%
21 CFR 820.72(a)# of observations 45; Percentage 7%

DES
(294 total)
21 CFR 820.30(g) # of observations 79; Percentage 27%
21 CFR 820.30(i) # of observations 59; Percentage 20%
21 CFR 820.30(a) # of observations 35; Percentage 12%

DOC
(223 total)
21 CFR 820.184 # of observations 101; Percentage 45%
21 CFR 820.40 # of observations 48; Percentage 22%
21 CFR 820.181 # of observations 38; Percentage 17%

MGMT
(280 total)
21 CFR 820.22 # of observations 106; Percentage 38%
21 CFR 820.20(c) # of observations 64; Percentage 23%
21 CFR 820.25(b) # of observations 55; Percentage 20%