Ok i see what you meant...
On your picture, it’s a basic IX (without any letter after, it’s a IX A)
The type IX A in OM has only one flak like your first picture.
What we can see, is that it’s doesn’t match the sub drawing of your second picture in the crew management...but the good thing is the flak slot correspond to what you get ingame (2 guys per flak gun)
So only problem is the drawing mismatching...to me, it seems to be a type IXB (if i recall well, the basic IXB has one flak upstairs and one flak on deck)
Right now, i dunno how to fix it, nor if there is any IX A drawing available...so best for the moment is to ignore the drawings in crew management tab
Thanks Peter for reporting this
ÉDIT: if i knew where to find the drawing file within the tons of files, there is an easy fix i could do with photoshop...but i suspect type IXB share the same file with type IXA...so either one or other would have wrong drawing...