bug is new in 6.06.00RC1, not present in 6.05.06
human, some stats (15 pt build)
Class: Aristocrat 1
Class: Bard: +1, +1, +1 (for Bard 3)
Bard 3 is 4th HD so gets +1 to Ability (Cha)
Class: Rogue +1
in 6.05.06 and earlier this is fine;
in 6.06.00RC1 the "todo" list now shows the "Add 2 +4s, 2 +2s, 1 -2" ability tweaks, which are normally applied to a creature with Racial HD which takes PC class levels.
pathfinder core supplements rule-set
Technically, code issue since the converter caused the improper combination.