diff --git a/CHANGELOG.md b/CHANGELOG.md
index c658e024d3a..c7b0088dc52 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,7 @@
 
 ## **[Unreleased]**
 
+- [#992](https://github.com/wasmerio/wasmer/pull/992) Updates WAPM version to 0.4.1, fix arguments issue introduced in #990
 - [#990](https://github.com/wasmerio/wasmer/pull/990) Default wasmer CLI to `run`.  Wasmer will now attempt to parse unrecognized command line options as if they were applied to the run command: `wasmer mywasm.wasm --dir=.` now works!
 - [#987](https://github.com/wasmerio/wasmer/pull/987) Fix `runtime-c-api` header files when compiled by gnuc.
 
diff --git a/src/bin/wasmer.rs b/src/bin/wasmer.rs
index 26afcc03947..36e0100d671 100644
--- a/src/bin/wasmer.rs
+++ b/src/bin/wasmer.rs
@@ -18,7 +18,7 @@ use std::process::exit;
 use std::str::FromStr;
 
 use std::collections::HashMap;
-use structopt::StructOpt;
+use structopt::{clap, StructOpt};
 
 use wasmer::*;
 use wasmer_clif_backend::CraneliftCompiler;
@@ -848,8 +848,19 @@ fn get_compiler_by_backend(backend: Backend) -> Option<Box<dyn Compiler>> {
 }
 
 fn main() {
-    let options = CLIOptions::from_iter_safe(env::args())
-        .unwrap_or_else(|_| CLIOptions::Run(Run::from_args()));
+    // We try to run wasmer with the normal arguments.
+    // Eg. `wasmer <SUBCOMMAND>`
+    // In case that fails, we fallback trying the Run subcommand directly.
+    // Eg. `wasmer myfile.wasm --dir=.`
+    let options = CLIOptions::from_iter_safe(env::args()).unwrap_or_else(|e| {
+        match e.kind {
+            // This fixes a issue that:
+            // 1. Shows the version twice when doing `wasmer -V`
+            // 2. Shows the run help (instead of normal help) when doing `wasmer --help`
+            clap::ErrorKind::VersionDisplayed | clap::ErrorKind::HelpDisplayed => e.exit(),
+            _ => CLIOptions::Run(Run::from_args()),
+        }
+    });
     match options {
         CLIOptions::Run(options) => run(options),
         #[cfg(not(target_os = "windows"))]
diff --git a/wapm-cli b/wapm-cli
index c2da5cda3b8..3562d6dda52 160000
--- a/wapm-cli
+++ b/wapm-cli
@@ -1 +1 @@
-Subproject commit c2da5cda3b8f9cf7dcea144f8cabdf342f38a0bf
+Subproject commit 3562d6dda52df526e6e1917dd33bb2454917ab9c