diff --git a/src/resources/extensions/gsd/auto-worktree.ts b/src/resources/extensions/gsd/auto-worktree.ts
index a0275619a..49696e308 100644
--- a/src/resources/extensions/gsd/auto-worktree.ts
+++ b/src/resources/extensions/gsd/auto-worktree.ts
@@ -188,8 +188,10 @@ function clearProjectRootStateFiles(basePath: string, milestoneId: string): void
     try {
       unlinkSync(file);
     } catch (err) {
-      /* non-fatal — file may not exist */
-      logWarning("worktree", `file unlink failed: ${err instanceof Error ? err.message : String(err)}`);
+      // ENOENT is expected — file may not exist (#3597)
+      if ((err as NodeJS.ErrnoException).code !== "ENOENT") {
+        logWarning("worktree", `file unlink failed: ${err instanceof Error ? err.message : String(err)}`);
+      }
     }
   }
 
@@ -218,8 +220,11 @@ function clearProjectRootStateFiles(basePath: string, milestoneId: string): void
             try {
               unlinkSync(join(basePath, f));
             } catch (err) {
-              /* non-fatal */
-              logWarning("worktree", `untracked file unlink failed: ${err instanceof Error ? err.message : String(err)}`);
+              // ENOENT/EISDIR are expected for already-removed or directory entries (#3597)
+              const code = (err as NodeJS.ErrnoException).code;
+              if (code !== "ENOENT" && code !== "EISDIR") {
+                logWarning("worktree", `untracked file unlink failed: ${err instanceof Error ? err.message : String(err)}`);
+              }
             }
           }
         }
diff --git a/src/resources/extensions/gsd/worktree-manager.ts b/src/resources/extensions/gsd/worktree-manager.ts
index b73e4e5ee..d8eb3760a 100644
--- a/src/resources/extensions/gsd/worktree-manager.ts
+++ b/src/resources/extensions/gsd/worktree-manager.ts
@@ -89,7 +89,9 @@ function normalizePathForComparison(path: string): string {
  */
 export function resolveGitDir(basePath: string): string {
   const gitPath = join(basePath, ".git");
-  if (!existsSync(gitPath)) return join(basePath, ".git");
+  if (!existsSync(gitPath)) return gitPath;
+  // In a normal repo .git is a directory — skip the file read (#3597)
+  if (lstatSync(gitPath).isDirectory()) return gitPath;
   try {
     const content = readFileSync(gitPath, "utf-8").trim();
     if (content.startsWith("gitdir: ")) {
@@ -98,7 +100,7 @@ export function resolveGitDir(basePath: string): string {
   } catch (e) {
     logWarning("worktree", `.git file read failed: ${(e as Error).message}`);
   }
-  return join(basePath, ".git");
+  return gitPath;
 }
 
 export function worktreesDir(basePath: string): string {