Some of the pebbles at the bottom of rivers and oceans are not waterlogged and create a pocket of water around them, while other pebbles are working fine.
At times i also find them spawning at the bottom of tall grass blocks.

I've reworked some code for the next update that should hopefully solve this. If not, the only other thing I can do at this point is make pebbles "Tick" (like redstone ore or crops), which just seems a bit overkill.

At times i also find them spawning at the bottom of tall grass blocks.

I have no idea how. I literally clear the block above the place I place the sample: