Haven’t experience this with grenades or flares, but have with compressed gas bottles. I will run up to a tank or harvester after giving him the EMP treatment to place a bottle by his feet. The placement animation runs, but it’s hit or miss whether it will actually drop it or not. Typically I have to do it a second time for it to work.
Ditto when placing a canister down with a radio / boombox for a trap. I place the canister down first, and sometimes it won’t place on the first try, despite the animation playing. At first I thought it was a collision thing with the machines not letting me place, but then I realized it was happening even trying to place one on clear ground.
I’m playing on PC.