We have a Magus with Bladebound Archetype.
UM p.47 states that the Black Blade feature replaces the magus Arcana gained at 3rd level.
Magus has been advenced through several PCGen versions. Last updated to L9 in 6.05.06 (attached). 6.05.06 shows the Magus Arcana pool as "2 remaining 0" (as expected).
When the attached file is opened in 6.06.00RC1, PCGen claims it has too many Magus Arcana, and shows the pool size as "1 remaining -1".
pathfinder core supplements ruleset