When the /fill command is used to replace water with lava, it acts rather oddly. The bug only occurs when you actually use the "replace" argument, a normal fill command works fine.
Replacing lava with water doesn't cause this bug, but you can get an "unknown error" message if the selection was large enough.
To reproduce:
Step 1: In a large body of water, use the following command:
/fill ~-50 ~ ~-50 ~50 ~ ~50 lava 0 replace water
Step 2: Be extremely confused.
Relates to MC-49545.
Is this still an issue in the most recent versions (currently that is 1.10.2, or 16w43a) of Minecraft? If so, please update the affected versions and help us keeping this ticket updated from time to time. If you are the owner/reporter of this ticket, you can modify the affected version(s) yourself.