I am using MythicCrucible latest version and also had this on all Artifacts versions I have worked through. Here is a video of the issue https://www.youtube.com/watch?v=7AmxYm90GvI&feature=youtu.be
if you put an item with a skill that activates with ~onSwing on your off-hand and you throw an item, it just activates the skill. There is a clear visible swinging animation that happens when you throw an item and that is simply how vanilla MC works IIRC. I think the onSwing should be changed from detecting swining to detecting a left click simply. I haven't done java so I'm not sure exactly how this would work but another way I suppose is to not count the onSwing if the swing is triggered by throwing an item.
This gets super irritating on my server where all abilities are activated by a left click and your inventory is constantly full so you just always activate your ability everytime you try empty your inventory out and then you are set on a cooldown. Here is my item and it's skills https://pastebin.com/CU5p0duh
Thanks!