I have found one of the references that I remember reading of, concerning a US sub being attacked by an IJN DD with torpedoes. In "Silent Victory" by Clay Blair Jr on Page 310 in my paperback version, near the bottom of the page is this:
A few nights later, he made a night surface approach on a convoy of two destroyers and three tankers. Before he could get off a shot, one of the destroyers sighted Gudgeon and charged, firing a torpedo. Stovall went deep.
The attack originated with Stovall's deck watch spotting a DD about 2145 while on the surface, and turned to approach it for attack, and while approaching, found another DD and an unidentified merchant, which they then turned to attack. The composition of the rest of the convoy was unknown at the time:
2156 First destroyer was observed to change course abruptly and head directly for us, range 3000-4000 yards. Made quick dive to avoid and rigged for depth charge attack. Changed course right to 130T. Went deep.
... which is a quote from his patrol report for the evening of 24 July, 1942. He makes no immediate mention of a countering torpedo attack, but further on he states:
Chief Torpedoman reported that he, and other personnel in torpedo room, heard what sounded like the high speed screws of a torpedo pass above torpedo room, as we passed 150 feet going down on this dive.
Of note is that the sonarman did not generate a warning - the torpedo room personnel heard it as it passed overhead. Neither the conning tower nor the control room personnel heard them - though there was probably a good bit of discussion "noise" going on with orders and acknowledgements, as they're diving for avoidance while rigging for depth charge attack.
I'm reasonably sure I read another report about one, but I might be remembering one of those WW2 sub movies...
