/fill...replace fails to remove water from waterlogged blocks

In short ... By using a command like / fill to remove water from a particular location, blocks other than just water are not cleaned and remain as water sources. Here is an example:

1) I will empty some of the water from this building, preserving only the structure.

2) This is the command I will use:
(It means that I will replace all water blocks with air.)
 

3) After executing the command, I noticed that there were still blocks of water.

4) Looking closer I could see that it was the blocks of grass that made the bug.

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The summary of the command used is as follows:
"/ fill xa ya za xb yb zb air 0 replace water"

In the example, the water is not gone because there is something besides the water itself.