diff --git a/backend/src/app/binfile/cleaner.clj b/backend/src/app/binfile/cleaner.clj
index 1f27e7751b..74c394e2fe 100644
--- a/backend/src/app/binfile/cleaner.clj
+++ b/backend/src/app/binfile/cleaner.clj
@@ -90,13 +90,18 @@
       (fix-root-shape)
       (fix-legacy-flex-dir)))
 
+(defn- fix-container
+  [container]
+  (-> container
+      ;; Remove possible `nil` keys on objects
+      (d/update-when :objects dissoc nil)
+      (d/update-when :objects d/update-vals clean-shape-post-decode)))
+
 (defn clean-file
   [file & {:as _opts}]
-  (let [update-container
-        (fn [container]
-          (d/update-when container :objects d/update-vals clean-shape-post-decode))]
-    (update file :data
-            (fn [data]
-              (-> data
-                  (update :pages-index d/update-vals update-container)
-                  (update :components d/update-vals update-container))))))
+  (update file :data
+          (fn [data]
+            (-> data
+                (d/update-when :pages-index d/update-vals fix-container)
+                (d/update-when :components d/update-vals fix-container)
+                (d/without-nils)))))
diff --git a/backend/src/app/tasks/file_gc.clj b/backend/src/app/tasks/file_gc.clj
index daa3d60038..e2358061d7 100644
--- a/backend/src/app/tasks/file_gc.clj
+++ b/backend/src/app/tasks/file_gc.clj
@@ -10,6 +10,7 @@
   file is eligible to be garbage collected after some period of
   inactivity (the default threshold is 72h)."
   (:require
+   [app.binfile.cleaner :as bfl]
    [app.binfile.common :as bfc]
    [app.common.files.helpers :as cfh]
    [app.common.files.validate :as cfv]
@@ -258,6 +259,7 @@
   (if-let [file (get-file cfg file-id)]
     (let [file (->> file
                     (bfc/decode-file cfg)
+                    (bfl/clean-file)
                     (clean-media! cfg)
                     (clean-fragments! cfg))
           file (assoc file :has-media-trimmed true)]