Buckets almost always hop into a different hotbar/inventory slot when filled with mana. My theory as to why this happens is because when you fill it, it gives you the bucket of mana, then destroys the bucket. The problem is that the bucket was still in that hotbar slot when the mana bucket was recieved, so it goes into a different slot. Doing those 2 things in the opposite order (destroy bucket, give mana bucket) would (presumably) fix this.