Video evidence:
https://clips.twitch.tv/SuspiciousCleverOwlCopyThis

This happened with Thermal Dynamics pipes and with Extra Utilities 2 Transfer Nodes,

I tested this in my world some. It appears the crucible isn't updating visually/WAILA, but TheOneProbe does get updated, and the lava is actually coming from the fluiduct's internal buffer.

I've attached some screen shots where I set up your conditions, then drained the stuff remaining in the fluiduct, then it stopped filling, but visually and in WAILA showed more fluid in the crucible.

My guess is that the tank.drain() call isn't being feed up to the crucible telling it to update the client (WAILA compat is @SideOnly(Side.CLIENT)). Haven't dug into TOP, but I bet it talks to the server more.

Repeatedly break and replace the barrel to drain liquid

Crucible is empty according to TOP, the duct is empty so the barrel no longer fills, but WAILA and the visuals says it still has lava.

Thanks for reporting, fixed it.