Playing with it now, under some conditions, using the new flechette doesn't actually take it from my inventory, or make a sound when I use it. It still gets used though. I don't recall this ever happening before.
Attached is a demo recorded with GZDoom version g4.4.2-m, Arch Linux 64-bit build.
Playing the demo normally (gzdoom -iwad hexen.wad -playdemo mageflechette.lmp) should show me picking up some flechettes and then using them on moving water. Everything works normally.
Playing with the mod (-file hexen_plums.wad) does the same thing except the flechettes stay in my inventory. The demo doesn't show it, but in most cases they work as you'd expect. Standing on moving water against the grate was the only reliable condition I could find to replicate it, but it happens other times as well.
Here is the relevant decorate: