Because it's not just Citizens that uses NPCs.

src/main/java/com/gmail/nossr50/skills/acrobatics/AcrobaticsEventHandler.java

@@ -53,7 +53,7 @@ public abstract class AcrobaticsEventHandler {
      * @return true if the damage is fatal, false otherwise
      */
     protected boolean isFatal(int damage) {
-        if (Misc.isCitizensNPC(player) || player.getHealth() - damage < 1) {
+        if (Misc.isNPC(player) || player.getHealth() - damage < 1) {
             return true;
         }
 

src/main/java/com/gmail/nossr50/skills/acrobatics/AcrobaticsManager.java

@@ -22,7 +22,7 @@ public class AcrobaticsManager extends SkillManager {
      * @param event The event to check
      */
     public void rollCheck(EntityDamageEvent event) {
-        if (Misc.isCitizensNPC(player) || !Permissions.roll(player)) {
+        if (Misc.isNPC(player) || !Permissions.roll(player)) {
             return;
         }
 
@@ -62,7 +62,7 @@ public class AcrobaticsManager extends SkillManager {
      * @param event The event to check
      */
     public void dodgeCheck(EntityDamageEvent event) {
-        if (Misc.isCitizensNPC(player) || !Permissions.dodge(player)) {
+        if (Misc.isNPC(player) || !Permissions.dodge(player)) {
             return;
         }
 

src/main/java/com/gmail/nossr50/skills/archery/ArcheryManager.java

@@ -20,7 +20,7 @@ public class ArcheryManager extends SkillManager {
      * @param livingEntity Entity damaged by the arrow
      */
     public void trackArrows(LivingEntity livingEntity) {
-        if (Misc.isCitizensNPC(player) || !Permissions.trackArrows(player)) {
+        if (Misc.isNPC(player) || !Permissions.trackArrows(player)) {
             return;
         }
 
@@ -45,7 +45,7 @@ public class ArcheryManager extends SkillManager {
      * @param event The event to modify
      */
     public void dazeCheck(Player defender, EntityDamageEvent event) {
-        if (Misc.isCitizensNPC(player) || !Permissions.daze(player)) {
+        if (Misc.isNPC(player) || !Permissions.daze(player)) {
             return;
         }
 
@@ -70,7 +70,7 @@ public class ArcheryManager extends SkillManager {
      * @param event The event to modify.
      */
     public void bonusDamage(EntityDamageEvent event) {
-        if (Misc.isCitizensNPC(player) || !Permissions.archeryBonus(player)) {
+        if (Misc.isNPC(player) || !Permissions.archeryBonus(player)) {
             return;
         }
 

src/main/java/com/gmail/nossr50/skills/mining/MiningManager.java

@@ -27,7 +27,7 @@ public class MiningManager extends SkillManager{
      * @param plugin mcMMO plugin instance
      */
     public void detonate(PlayerInteractEvent event) {
-        if (Misc.isCitizensNPC(player)) {
+        if (Misc.isNPC(player)) {
             return;
         }
 
@@ -62,7 +62,7 @@ public class MiningManager extends SkillManager{
      * @param event Event whose explosion is being processed
      */
     public void blastMiningDropProcessing(EntityExplodeEvent event) {
-        if (Misc.isCitizensNPC(player)) {
+        if (Misc.isNPC(player)) {
             return;
         }
 
@@ -87,7 +87,7 @@ public class MiningManager extends SkillManager{
      * @param event Event whose explosion damage is being reduced
      */
     public void demolitionsExpertise(EntityDamageEvent event) {
-        if (Misc.isCitizensNPC(player)) {
+        if (Misc.isNPC(player)) {
             return;
         }
 
@@ -104,7 +104,7 @@ public class MiningManager extends SkillManager{
      * @param event Event whose explosion radius is being changed
      */
     public void biggerBombs(ExplosionPrimeEvent event) {
-        if (Misc.isCitizensNPC(player)) {
+        if (Misc.isNPC(player)) {
             return;
         }