Plugin just doesn't work, when I start the server it appears:

Ambiguous plugin name CommandNPC' for files plugins\CommandNPC.jar' and plugins\CommandNPC-1.9.1.jar' in plugins'
Could not load 'plugins\PermissionsEx-1.23.3.jar' in folder 'plugins'

What do I do?

Make sure you remove old commandnpc jar file if you recently updated

Also, what version is your server?

I have never used older versions on this server.
and my server is 1.8.X

Ambiguous plugin name CommandNPC' for files plugins\CommandNPC.jar' and plugins\CommandNPC-1.9.1.jar' in plugins'
Could not load 'plugins\PermissionsEx-1.23.3.jar' in folder 'plugins'

From wha to could see. You have 2 different CommandNPC in the plugin folder.

Could not load 'plugins\CommandNPC-1.9.1.jar' in folder 'plugins'
org.bukkit.plugin.UnknownDependencyException: Citizens
at org.bukkit.plugin.SimplePluginManager.loadPlugins(SimplePluginManager.java:219) [latest1.jar:git-Spigot-db6de12-18fbb24]
at org.bukkit.craftbukkit.v1_8_R3.CraftServer.loadPlugins(CraftServer.java:292) [latest1.jar:git-Spigot-db6de12-18fbb24]
at net.minecraft.server.v1_8_R3.DedicatedServer.init(DedicatedServer.java:198) [latest1.jar:git-Spigot-db6de12-18fbb24]
at net.minecraft.server.v1_8_R3.MinecraftServer.run(MinecraftServer.java:525) [latest1.jar:git-Spigot-db6de12-18fbb24]
at java.lang.Thread.run(Unknown Source) [?:1.8.0_261]

Could not load 'plugins\CommandNPC-1.9.1.jar' in folder 'plugins'
org.bukkit.plugin.UnknownDependencyException: Citizens

You need Citizens plugin for using CommandNPC