The /fill console command is offset by 1 to the east compared to the F3 screen's coordinates.

For Example, what I see as being -110 64 5 is instead -109 64 5. I have added images to demonstrate

In fullsizeoutput_1 and _2 I run the command:
/fill -110 63 5 -110 32 -49 end_stone_bricks replace minecraft:water

and in _3 I run the opposite command.
/fill -110 63 5 -110 32 -49 minecraft:water replace end_stone_bricks

All with the F3 screen up in order to see the difference in coordinates.