So just to clarify do you mean occasions when German U-Boats engaged each other in a friendly fire incident, or just in general submarine on submarine combat during WW2?

If you're talking about submarine battles, it happened rarely but did occur. HMS Venturer, however, was the only one I believe to sink another one (U-864) while both were submerged (in February 1945), but also sank U-771 which was not submerged in November 1944. Actually, a lot of U-boats ended on the wrong side of encounters with Allied boats, if the reviled Wikipedia is to be believed. But of course this doesn't include inconclusive encounters, or ones where the German vessel came out on top.

In the Pacific, USS Gudgeon sank the surfaced Japanese I-73 in January 1942; at least five other Japanese submarines were lost to US counterparts (I-28, 29, 168, 183, and Ro-45), but no US submarines were lost to I-boats that I've seen. I'm not sure about other combatants in that theater, however.

So yes, in short, there were definitely engagements between submarines, although how pitched these battles might have been, and how much was just sheer opportunity, it's hard to say. The kind of duel we associate with modern attack boats would have been a good bit more difficult in the Second World War, which may be why it only once resulted in a decisive action.