As confirmed by Graalx2 here, the issues with legacy upgrades are being fixed.

Unaware of what the issues were? A number of legacies (at least eight of them confirmed for Wardens!) did not reduce in cost at certain upgrade levels. (In particular, T4>T5 and T5>T6 were being miscalculated.) That means that, given a rate of something like 500SM/hr (taking into account dailies), you were looking at about four hours of wasted gameplay upon purchase of a Scroll of Entitlement, because your legacy tier upgrade would net you zero points. Oops.

Glad to see this is being fixed. Doubly glad to see the devs communicating with us. :)