After using a warpstone I sometimes find it that my demigod refuses to perform command for something like 3 secs.
For example I was playing as Sedna, focused on pounce and they tried to warp in + pounce, It does work most of the times but a few times she just stood there doing nothing, I then tried to order her to move back but she didnt, took like 4 seconds before she even moved.
I would say this happens like once in three times you try any warp combo.