Infinite water generator is created if two blocks of water are across the same block and on solid blocks. The trapdoors also keep water out, but don`t create an infinite generator if are placed at bottom of block with water.

Possible explanation:

The code that is responsible for the movement of water does not allow it to flow through the trapdoors in the blocks where it is located, but the code responsible for the infinite water generator may think that there is a void under the water and it should not be generated