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.
[media]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.
[media]4) Looking closer I could see that it was the blocks of grass that made the bug.
[media]------
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.
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I am not sure what is intended in this case, I will leave that up to Mojang and their Dev team to decide.
The behaviour is partially the same in the Java edition, except that when using the fill command without replacing blocks, the water and the waterlogged blocks get removed at the same time.
Also affects Win 10 Bedrock version 1.12.1 with server 1.12.1 (Ubuntu)
I ran into this when cloning a shipwreck to be above the water and then tried to use /fill to replace the water with air.
It seems to mainly affect non-cube blocks, although some cube blocks seemed to be waterlogged.
Anything affected had to be manually removed, use /fill to replace with air, and then add the block back.
Also affects Java version 1.14.4
It's the same problem as Rob Edgler's comment about Win 10 Bedrock version 1.12.1
It seems to deal with the new waterlogged blocks as they are not considered "water" but sea grass with water in it.
Work around: Replace all sea grass with air, then replace all water with air.