Since I purchased the game the night before traveling for the holidays, I didn't get a chance to play yet. If what you're saying is what I think you're saying, I'm feeling a little disheartened about starting.
I'll try to explain what I think you're talking about, correct me if I'm wrong:
You hit button "1" to cast something that takes 2 seconds to cast. However, due to this issue, the target actually receives the damage or healing 2.5 or 3.0 seconds after you started casting (due to damage/healing not applying until a certain point in the animation). During that 0.5 or 1.0 second "extra time", your buddy who was being healed could be killed by the mob, or the boss you were fighting could have killed you, even though your heal/damage would have been enough to save/kill the target if it would have applied at the 2.0 second mark instead of the 2.5 second mark.
Sorry if this is confusing, but I am trying to understand. If this is the case, it's a game breaker for me. Coming from raiding in WoW, things need to happen very specifically and precisely as you activate them. Actions advertised as "this effect happens after 3 seconds of cast time" should never actually mean "this effect happens after 3.5 or 4.0 seconds of cast time."