/// api_version=2

...
code

This will fix the issue.
See: https://liquidbounce.net/docs/ScriptAPI/Getting Started

Also fixed in future versions by removing support for ScriptAPI v1:
https://github.com/CCBlueX/LiquidBounce/commit/3e92903f1372e1c96225bca057f0f136928d3bd5

0 1zun4 committed to CCBlueX/LiquidBounce

removed support for ScriptAPI v1

Please update your script to ScriptAPI v2 to avoid issues in the future.
See https://liquidbounce.net/docs/ScriptAPI/Getting%20Started for further information.

This change fixes module and command manager not being defined correctly.
See https://forums.ccbluex.net/topic/7671/why-i-can-t-use-commandmanager-or-modulemanager-in-my-script/

try {
    Chat.print(typeof(scriptManager)); // object
    Chat.print(JSON.stringify(scriptManager)); // undefined
    scriptManager.unloadScripts();
    Chat.print("done"); // works
}catch (e) {
    Chat.print(e);
}


try {
    Chat.print(typeof(commandManager)); // [object]
    Chat.print(JSON.stringify(commandManager)); // {}
    commandManager.registerCommands(); // not working -> TypeError: commandManager.registerCommands is not a function
    commandManager.executeCommands('killaura range 3.4'); // not working, stopped above
}catch (e) {
    Chat.print(e);
}

try {
    Chat.print(typeof(moduleManager)); // [object]
    Chat.print(JSON.stringify(moduleManager)); // {}
    moduleManager.registerModules(); // not working -> TypeError: moduleManager.registerModules is not a function
    moduleManager.getModule('KillAura').setState(false); // not working, stopped above
}catch (e) {
    Chat.print(e);
}

After changing the variable name of commandManager and moduleManager to pickaxe and stone it suddenly worked!

scriptEngine.put("stone", moduleManager)
scriptEngine.put("pickaxe", commandManager)
scriptEngine.put("scriptManager", scriptManager)

So it seems to be conflicting with something else.

Oh my god... I realized. It was caused by the ScriptAPI v1 legacy support script. >(

    this.moduleManager = Java.type("net.ccbluex.liquidbounce.LiquidBounce").moduleManager;
    this.Module = Java.type("net.ccbluex.liquidbounce.features.module.Module");
    this.ArrayList = Java.type("java.util.ArrayList");

since everything is in kotlin now, you most likely have to do moduleManager.INSTANCE.getModule()
commandManager.INSTANCE....

however this may be subject to change in the future because the documentation doesn't show this and it's not good

https://github.com/CCBlueX/LiquidBounce/blob/legacy/src/main/java/net/ccbluex/liquidbounce/script/Script.kt#L59-L63

I will look into this.