I'll just give the answer to mine, since nobody has gotten it yet.

It is turret29 on the Hatshepsut, which is centered on the upper rear section; I actually posted a thread about it a long time ago. You need to look very closely in Modelview or something to notice it, but it severely inhibits the turret's field of view in the game and makes it act really weird, which is how I found it. Unfortunately, I don't know how to move the actual turret submodel around, so I cannot affect a fix.
GTM Hippocrates, turret 5, on the lower aft section. There is a turret on the outside starboard face of that component, but the port side turret is placed inside the hull.
I just checked this and you are quite right here too; guess this is another ship with the same problem. Interestingly, the turret4 on the opposite side (which is essentially a mirror of the turret5 side) is fine.