diff --git a/cli/tools/registry/mod.rs b/cli/tools/registry/mod.rs
index 3d13a52b77..de319281b5 100644
--- a/cli/tools/registry/mod.rs
+++ b/cli/tools/registry/mod.rs
@@ -212,8 +212,15 @@ fn collect_excluded_module_diagnostics(
     return;
   };
   let specifiers = graph
-    .specifiers()
-    .map(|(s, _)| s)
+    .modules()
+    .filter_map(|m| match m {
+      deno_graph::Module::Js(_) | deno_graph::Module::Json(_) => {
+        Some(m.specifier())
+      }
+      deno_graph::Module::Npm(_)
+      | deno_graph::Module::Node(_)
+      | deno_graph::Module::External(_) => None,
+    })
     .filter(|s| s.as_str().starts_with(root.as_str()));
   for specifier in specifiers {
     if !file_patterns.matches_specifier(specifier) {
diff --git a/tests/specs/publish/byonm_dep/__test__.jsonc b/tests/specs/publish/byonm_dep/__test__.jsonc
new file mode 100644
index 0000000000..303718c998
--- /dev/null
+++ b/tests/specs/publish/byonm_dep/__test__.jsonc
@@ -0,0 +1,4 @@
+{
+  "args": "publish --dry-run --allow-dirty",
+  "output": "publish.out"
+}
diff --git a/tests/specs/publish/byonm_dep/deno.jsonc b/tests/specs/publish/byonm_dep/deno.jsonc
new file mode 100644
index 0000000000..37a2377308
--- /dev/null
+++ b/tests/specs/publish/byonm_dep/deno.jsonc
@@ -0,0 +1,11 @@
+{
+  "name": "@scope/package",
+  "version": "0.0.0",
+  "exports": "./mod.ts",
+  "publish": {
+    // this was previously causing issues because it would cause
+    // external modules in the node_modules directory to be ignored
+    "include": ["mod.ts"]
+  },
+  "unstable": ["byonm", "sloppy-imports"]
+}
diff --git a/tests/specs/publish/byonm_dep/mod.ts b/tests/specs/publish/byonm_dep/mod.ts
new file mode 100644
index 0000000000..b7c276fd49
--- /dev/null
+++ b/tests/specs/publish/byonm_dep/mod.ts
@@ -0,0 +1,7 @@
+import { add } from "package";
+
+export function myAdd(a: number, b: number): number {
+  return add(a, b);
+}
+
+export { add };
diff --git a/tests/specs/publish/byonm_dep/node_modules/package/index.d.ts b/tests/specs/publish/byonm_dep/node_modules/package/index.d.ts
new file mode 100644
index 0000000000..9b197eb1e4
--- /dev/null
+++ b/tests/specs/publish/byonm_dep/node_modules/package/index.d.ts
@@ -0,0 +1 @@
+export function add(a: number, b: number): number;
diff --git a/tests/specs/publish/byonm_dep/node_modules/package/index.js b/tests/specs/publish/byonm_dep/node_modules/package/index.js
new file mode 100644
index 0000000000..0ecf3b8750
--- /dev/null
+++ b/tests/specs/publish/byonm_dep/node_modules/package/index.js
@@ -0,0 +1,3 @@
+export function add(a, b) {
+  return a + b;
+}
\ No newline at end of file
diff --git a/tests/specs/publish/byonm_dep/node_modules/package/package.json b/tests/specs/publish/byonm_dep/node_modules/package/package.json
new file mode 100644
index 0000000000..07fe062282
--- /dev/null
+++ b/tests/specs/publish/byonm_dep/node_modules/package/package.json
@@ -0,0 +1,4 @@
+{
+  "main": "index.js",
+  "type": "module"
+}
\ No newline at end of file
diff --git a/tests/specs/publish/byonm_dep/package.json b/tests/specs/publish/byonm_dep/package.json
new file mode 100644
index 0000000000..f0b3ee21dd
--- /dev/null
+++ b/tests/specs/publish/byonm_dep/package.json
@@ -0,0 +1,5 @@
+{
+  "dependencies": {
+    "package": "*"
+  }
+}
diff --git a/tests/specs/publish/byonm_dep/publish.out b/tests/specs/publish/byonm_dep/publish.out
new file mode 100644
index 0000000000..f3b8a0dccd
--- /dev/null
+++ b/tests/specs/publish/byonm_dep/publish.out
@@ -0,0 +1,6 @@
+Check file:///[WILDLINE]/mod.ts
+Checking for slow types in the public API...
+Check file:///[WILDLINE]/mod.ts
+Simulating publish of @scope/package@0.0.0 with files:
+   file:///[WILDLINE]/mod.ts (129B)
+Warning Aborting due to --dry-run