S2 tells how the plot holes is connected. Seems like everything has been planned by the author
I highly doubt that everything was planned by Kubo from the beginning, however he and his team did a good job of filling those narrative holes.
@camimaou I agree with what you are saying especially with this recent episode. I feel like maybe the situation with Zangetsu and Ichigo's true Zanpaktou wasn't planned and at the same time it was, but at a later time. Either way I think it was a nice save.