diff --git a/packages/babel-core/src/transformation/normalize-file.js b/packages/babel-core/src/transformation/normalize-file.js
index d7911cb0d0..ae2d9a1d8c 100644
--- a/packages/babel-core/src/transformation/normalize-file.js
+++ b/packages/babel-core/src/transformation/normalize-file.js
@@ -49,6 +49,9 @@ export default function normalizeFile(
       throw new Error("AST root must be a Program or File node");
     }
   } else {
+    // The parser's AST types aren't fully compatible with the types generated
+    // by the logic in babel-types.
+    // $FlowFixMe
     ast = parser(pluginPasses, options, code);
   }
 
diff --git a/packages/babel-template/src/parse.js b/packages/babel-template/src/parse.js
index 587668ae5f..9186780f1c 100644
--- a/packages/babel-template/src/parse.js
+++ b/packages/babel-template/src/parse.js
@@ -142,6 +142,7 @@ function parseWithCodeFrame(code: string, parserOpts: {}): BabelNodeFile {
   };
 
   try {
+    // $FlowFixMe - The parser AST is not the same type as the babel-types type.
     return parse(code, parserOpts);
   } catch (err) {
     const loc = err.loc;