Also found this issue. More specifically, it can occur when any 2 pieces of TNT overlap inside a water block (flowing or source) that has no block above it. Placing a block above the the water before the TNT is dispensed prevents the issue from happening. The cause appears to be to be TNT entities moving ever so slightly upwards when overlapped, but that's just a guess.
Namco Four
Also found this issue. More specifically, it can occur when any 2 pieces of TNT overlap inside a water block (flowing or source) that has no block above it.
Placing a block above the the water before the TNT is dispensed prevents the issue from happening.
The cause appears to be to be TNT entities moving ever so slightly upwards when overlapped, but that's just a guess.