diff --git a/lib/init-action.js b/lib/init-action.js
index 1ed7e5490..7b21c181c 100644
--- a/lib/init-action.js
+++ b/lib/init-action.js
@@ -92539,9 +92539,7 @@ async function run(startedAt) {
     const rawLanguages = getRawLanguagesNoAutodetect(
       getOptionalInput("languages")
     );
-    const useOverlayAwareDefaultCliVersion = !!analysisKinds?.includes(
-      "code-scanning" /* CodeScanning */
-    );
+    const useOverlayAwareDefaultCliVersion = analysisKinds?.length === 1 && analysisKinds[0] === "code-scanning" /* CodeScanning */;
     const initCodeQLResult = await initCodeQL(
       getOptionalInput("tools"),
       apiDetails,
diff --git a/lib/setup-codeql-action.js b/lib/setup-codeql-action.js
index 243a749cb..d3a585c78 100644
--- a/lib/setup-codeql-action.js
+++ b/lib/setup-codeql-action.js
@@ -89533,7 +89533,7 @@ async function run(startedAt) {
       gitHubVersion.type,
       codeQLDefaultVersionInfo,
       rawLanguages,
-      analysisKinds.includes("code-scanning" /* CodeScanning */),
+      analysisKinds.length === 1 && analysisKinds[0] === "code-scanning" /* CodeScanning */,
       features,
       logger
     );
diff --git a/src/init-action.ts b/src/init-action.ts
index b529b6804..a6521f4f0 100644
--- a/src/init-action.ts
+++ b/src/init-action.ts
@@ -304,9 +304,9 @@ async function run(startedAt: Date) {
     const rawLanguages = configUtils.getRawLanguagesNoAutodetect(
       getOptionalInput("languages"),
     );
-    const useOverlayAwareDefaultCliVersion = !!analysisKinds?.includes(
-      AnalysisKind.CodeScanning,
-    );
+    const useOverlayAwareDefaultCliVersion =
+      analysisKinds?.length === 1 &&
+      analysisKinds[0] === AnalysisKind.CodeScanning;
     const initCodeQLResult = await initCodeQL(
       getOptionalInput("tools"),
       apiDetails,
diff --git a/src/setup-codeql-action.ts b/src/setup-codeql-action.ts
index c23553c98..86d4a9feb 100644
--- a/src/setup-codeql-action.ts
+++ b/src/setup-codeql-action.ts
@@ -152,7 +152,8 @@ async function run(startedAt: Date): Promise<void> {
       gitHubVersion.type,
       codeQLDefaultVersionInfo,
       rawLanguages,
-      analysisKinds.includes(AnalysisKind.CodeScanning),
+      analysisKinds.length === 1 &&
+        analysisKinds[0] === AnalysisKind.CodeScanning,
       features,
       logger,
     );