Advanced NME Warheads only requires 1 level of predecessor (NME Warheads). It should require two, since the second builds off of the first.

To express the bug: Start game as Vasari Rebel and look at the named research items.

To fix the bug: in file RESEARCHSUBJECT_ADVANCED_NME_WARHEADS, line 16, change the Level value to 2.

Prerequisites
    NumResearchPrerequisites 1
    ResearchPrerequisite
        Subject "RESEARCHSUBJECT_WEAPONDAMAGE_PHASEMISSILE0"
        Level 1 <- Changing this to 2 fixed it for me.

This change ensures that "increase damage from 5% to 10%" is researched before "increase damage from 10% to 15%."

EDIT: colored text is now visible.