The giant chance cube that launches arrows, fireballs, wither heads, tnt, etc.. glitches out and the wither skulls get stuck in the air on my Sky Factory 3.0.4 sub server. Images: http://imgur.com/a/Ffn1B

v2.3.3.135

Has been fixed and is slated for the next update when I can fix this last bug (and take a look at WAPC's crash log). in the mean time try running the command /kill @e [type=WitherSkull] double check that is right before actually trying it though xD