When using the /fill command to replace water with air, due to the new water mechanic, will not remove the water within any flooded blocks.
I understand that this wouldn't make sense for replacing water with any other block, but replacing with air (or lava if that ever becomes a thing in a future update) makes sense when trying to clear an area large scale (e.g. a ship wreck)
This also effects the usage of sponges which no longer removes water inside flooded blocks
Please check if that's still an issue in the latest 1.14 (pre-)release.