Got the bug where your Ninja Operative cannot have perks above Sergeant ?
Let me show you da way :

1) Go into this mod folder, should be someting like :

SteamLibrary\steamapps\workshop\content\268500\3474531591

Please not that i'm not familiar with how Steam Workshop works, so i'm not 100% sure if the numbers are exactly the same for everyone.
Another and simple way is to use AML and right clic into the mod name and then "Show in Explorer" :D

2) Then go into "Config" and open "XComAmalgamation.ini"
Again, you can simply open the config file from AML, but i am used to my text editor ^^

3) Search for the block :
;-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>
;<>-<>-<>-<>-<>-<>-<>-<>-<> Ninja Operative Primary <>-<>-<>-<>-<>-<>-<>-<>-<>-<>
;-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>-<>

4) Replace the content by this :

+PrimarySpecs=(Spec="NinjaOperative", \\
AllowedWeapons[0]=(WeaponType="Sword", SlotType=eInvSlot_PrimaryWeapon), \\
AllowedWeapons[1]=(WeaponType="psiamp", SlotType=eInvSlot_SecondaryWeapon), \\
AllowedWeapons[2]=(WeaponType="empty", SlotType=eInvSlot_SecondaryWeapon), \\
AllowedArmors[0]="NINJASUIT", \\
SpecIcon="img:///UILibrary_WOTCHeroIcons.NinjaClassIcon", \\
NicknameSrc="Ninja_Operative" \\
)

+AbilityDecks=(DeckName="NinjaOp_23", \\
Abilities=( \\
(AbilityName="NinjaMindOverBody"), \\
(AbilityName="NinjaLowProfile"), \\
(AbilityName="NinjaBlink"), \\
(AbilityName="NinjaAcrobatics"), \\
(AbilityName="SSShadowstrike", ApplyToWeaponSlot=eInvSlot_Unknown) \\
) \\
)

+AbilityDecks=(DeckName="NinjaOp_45", \\
Abilities=( \\
(AbilityName="NinjaAgility"), \\
(AbilityName="NinjaKunaiFaceoffDummy", ApplyToWeaponSlot=eInvSlot_TertiaryWeapon), \\
(AbilityName="SSPsiGuard"), \\
(AbilityName="NinjaRelocation"), \\
(AbilityName="NinjaBladesEnd", ApplyToWeaponSlot=eInvSlot_PrimaryWeapon) \\
) \\
)

+AbilityDecks=(DeckName="NinjaOp_67", \\
Abilities=( \\
(AbilityName="NinjaMasterOfShadows"), \\
(AbilityName="NinjaKunaiMastery", ApplyToWeaponSlot=eInvSlot_TertiaryWeapon), \\
(AbilityName="NinjaPreservation"), \\
(AbilityName="NinjaSense"), \\
(AbilityName="NinjaMasterSwordsman", ApplyToWeaponSlot=eInvSlot_PrimaryWeapon) \\
) \\
)

+AbilityDecks=(DeckName="NinjaOp_8", \\
Abilities=( \\
(AbilityName="NinjaTeleport", ApplyToWeaponSlot=eInvSlot_SecondaryWeapon), \\
(AbilityName="NinjaKunaiHailstormDummy", ApplyToWeaponSlot=eInvSlot_TertiaryWeapon), \\
(AbilityName="SSReaper", ApplyToWeaponSlot=eInvSlot_PrimaryWeapon) \\
) \\
)

+SpecDataset=(Spec="NinjaOperative", \\
Ranks[0] = ( \\
Skill = (AbilityName="NinjaTheWayOfTheNinja"), \\
Stats = ((StatType=eStat_HP,StatAmount=1), (StatType=eStat_Offense,StatAmount=2), (StatType=eStat_Defense,StatAmount=5), (StatType=eStat_Will,StatAmount=5), (StatType=eStat_Dodge,StatAmount=5), (StatType=eStat_PsiOffense,StatAmount=50), (StatType=eStat_CombatSims,StatAmount=1)) \\
), \\
Ranks[1] = ( \\
Deck = "NinjaOp_23", \\
Stats = ((StatType=eStat_Offense,StatAmount=3), (StatType=eStat_PsiOffense,RandStatAmount=5)) \\
), \\
Ranks[2] = ( \\
Deck = "NinjaOp_23", \\
Stats = ((StatType=eStat_HP,StatAmount=1), (StatType=eStat_Offense,StatAmount=3), (StatType=eStat_Will,StatAmount=2), (StatType=eStat_PsiOffense,RandStatAmount=5)) \\
), \\
Ranks[3] = ( \\
Deck = "NinjaOp_45", \\
Stats = ((StatType=eStat_Offense,StatAmount=3), (StatType=eStat_PsiOffense,RandStatAmount=5)) \\
), \\
Ranks[4] = ( \\
Deck = "NinjaOp_45", \\
Stats = ((StatType=eStat_HP,StatAmount=1), (StatType=eStat_Offense,StatAmount=3), (StatType=eStat_Will,StatAmount=2), (StatType=eStat_PsiOffense,RandStatAmount=5)) \\
), \\
Ranks[5] = ( \\
Deck = "NinjaOp_67", \\
Stats = ((StatType=eStat_HP,StatAmount=1), (StatType=eStat_Offense,StatAmount=3), (StatType=eStat_Will,StatAmount=2), (StatType=eStat_PsiOffense,RandStatAmount=5)) \\
), \\
Ranks[6] = ( \\
Deck = "NinjaOp_67", \\
Stats = ((StatType=eStat_HP,StatAmount=1), (StatType=eStat_Offense,StatAmount=3), (StatType=eStat_Will,StatAmount=2), (StatType=eStat_PsiOffense,RandStatAmount=5)) \\
), \\
Ranks[7] = ( \\
Deck = "NinjaOp_8", \\
Stats = ((StatType=eStat_Offense,StatAmount=3), (StatType=eStat_PsiOffense,RandStatAmount=10)) \\
) \\
)

5) Should be done, but it will only affect newly promoted Ninjas or you have to reroll your soldier with the Amalgamation console mod :)

Enjoy