It sounds like you might be unaware that every key-frame in sprite can have a totally different bone set-up, sprites and hierarchy... adding and removing bones at any single point in the timeline will only effect the timeline from that point where you made the change until the next key-frame. Not knowing this can of course cause unexpected results when adding or deleting bones, and changing parent/child relationships, expecting the changes to be animation wide, when the changes will in fact not be animation-wide.
Of course limbs being assigned momentarily to different or suddenly missing parent bones across the time line will cause them to move in strange ways, first obeying and tweening to one bone, and then suddenly a different one etc.
It's definitely a good idea to have your character properly boned in the first place before animating to avoid hierarchy confusion once there are many key frames, movements etc... its fine to add bones for new sprites, or change hierarchies mid animation, so long as you understand those changes are only in effect until the next key frame is reached...so if you want those new bones and the new hierarchy structure to continue for the remainder of the animation you must copy and paste the new bones to each successive key-frame.
