diff --git a/monai/transforms/transform.py b/monai/transforms/transform.py
index 1a365b8d8e..d9a16d53e7 100644
--- a/monai/transforms/transform.py
+++ b/monai/transforms/transform.py
@@ -143,10 +143,19 @@ def apply_transform(
     try:
         map_items_ = int(map_items) if isinstance(map_items, bool) else map_items
         if isinstance(data, (list, tuple)) and map_items_ > 0:
-            return [
-                apply_transform(transform, item, map_items_ - 1, unpack_items, log_stats, lazy, overrides)
-                for item in data
-            ]
+            res: list[Any] = []
+            for item in data:
+                res_item = apply_transform(transform, item, map_items_ - 1, unpack_items, log_stats, lazy, overrides)
+                # Only extend if we're at the leaf level (map_items_ == 1) and the transform
+                # actually returned a list (not preserving nested structure)
+                if isinstance(res_item, list) and map_items_ == 1:
+                    if not isinstance(item, (list, tuple)):
+                        res.extend(res_item)
+                    else:
+                        res.append(res_item)
+                else:
+                    res.append(res_item)
+            return res
         return _apply_transform(transform, data, unpack_items, lazy, overrides, log_stats)
     except Exception as e:
         # if in debug mode, don't swallow exception so that the breakpoint
@@ -482,8 +491,7 @@ def key_iterator(self, data: Mapping[Hashable, Any], *extra_iterables: Iterable
                 yield (key,) + tuple(_ex_iters) if extra_iterables else key
             elif not self.allow_missing_keys:
                 raise KeyError(
-                    f"Key `{key}` of transform `{self.__class__.__name__}` was missing in the data"
-                    " and allow_missing_keys==False."
+                    f"Key `{key}` of transform `{self.__class__.__name__}` was missing in the data and allow_missing_keys==False."
                 )
 
     def first_key(self, data: dict[Hashable, Any]):