The worst things I ever did was to sink a French merchant vessel (heavy fog) and a neutral Sampan (dumb luck).
There are two websites that I use (once in a while) for quick reference. One site lists 1 sub (Seawolf) as lost to friendly fire, the other lists 2 subs (Seawolf, Dorado) lost to friendly fire.
http://www.subsowespac.org/united-st...d-war-ii.shtml
http://www.valoratsea.com/losses1.htm
I'm not sure of how accurate or up to date the stats are on these pages.