In regards to "The War in the Atlantic", yes, there were a number. Look at the "Attacks on this Day" on the "Events on this Day" pages on this website. Particularly in the first 6 months of the war, air patrols were thin and poorly organized; there were a number of Typ II Uboots that were operating around the British Isles and they would often make the transit journeys near the German ports in the Nord See on the surface. Since the British submarines were also moving mostly unmolested, there was a good bit of contact between Uboots and British subs; however, these "attacks" usually amounted to misses with torpedoes, partly because the torpedoes in use by both sides were poor (hard to aim, not very accurate at running to the aim that they'd been launched, and warheads so poor that many were duds) and partly because crews were (relative to later in the War) not well trained and inexperienced. (See U-2,U-3,U-14,U-21,U-23,U-28,U-31,U-35,U-36,U-51,U-62,U-63,U-74,U-140, and U-144 Also, see HMS Spearfish, FR Doris, HMS Parthian, Soviet M-175, and HMS Thistle.)
There was at least on Uboot (and perhaps two) sunk by torpedoes in the Mediterranean (including U-95, sunk by a Dutch submarine, also HMS Triad) and at least one (and perhaps two) sunk in the eastern Indian Ocean (including U-168, also sunk by a Dutch submarine; also Dutch HrMs K XVI), near Indonesia and others (U-67,U-124,U-374 and the Italian Guglielmotti, HMS P-615, HMS Severn, HMS Rorqual)
There were a couple of notable successes by British subs in the North Sea later in the War (U-771, U-987, U-408/attacked, not hit) and a very famous example was the sinking of a Uboot as it was leaving a Norwegian harbor (U-864). It was located by sonar (or Asdic) by a British submarine, which fired a spread of torpedoes at it; at least one hit, resulting in the only known instance (TIKO) of a submarine being sunk by another when both were submerged.
Data on all these occurrences is listed on this website; also, see [www.uboatarchive.net] .

HTH, B Henderson North Carolina USA

(I think that there were some Allied/Japanese sub against sub attacks in the Pacific but I cannot comment on those.)