Just do not engage battleships in piers.The game doesn't take into account ships sank in swallow waters.

I sank a Ise in Yokosuka, she capsized but nothing happened,
I spent 4 torps for nothing

Ships even or smaller than Heavy Cruisers/large tankers seem to sink normally and you do get the kill.
I harbor raid alot but I never seen a minefield or a net.

I use TMO2+RSRDC
There are truly nasty and when I was playing SH3/GWX I never even got close to harbors.