diff --git a/src/Ryujinx.Ava/Common/ApplicationHelper.cs b/src/Ryujinx.Ava/Common/ApplicationHelper.cs
index 4349b442a743..20b8ac95bca2 100644
--- a/src/Ryujinx.Ava/Common/ApplicationHelper.cs
+++ b/src/Ryujinx.Ava/Common/ApplicationHelper.cs
@@ -235,9 +235,14 @@ public static async Task ExtractSection(NcaSectionType ncaSectionType, string ti
 
                     try
                     {
-                        IFileSystem ncaFileSystem = patchNca != null
-                            ? mainNca.OpenFileSystemWithPatch(patchNca, index, IntegrityCheckLevel.ErrorOnInvalid)
-                            : mainNca.OpenFileSystem(index, IntegrityCheckLevel.ErrorOnInvalid);
+                        bool sectionExistsInPatch = false;
+                        if (patchNca != null)
+                        {
+                            sectionExistsInPatch = patchNca.CanOpenSection(index);
+                        }
+
+                        IFileSystem ncaFileSystem = sectionExistsInPatch ? mainNca.OpenFileSystemWithPatch(patchNca, index, IntegrityCheckLevel.ErrorOnInvalid)
+                                                                         : mainNca.OpenFileSystem(index, IntegrityCheckLevel.ErrorOnInvalid);
 
                         FileSystemClient fsClient = _horizonClient.Fs;
 
diff --git a/src/Ryujinx.Ava/UI/Controls/ApplicationContextMenu.axaml b/src/Ryujinx.Ava/UI/Controls/ApplicationContextMenu.axaml
index 63153db43240..427e7ab27f05 100644
--- a/src/Ryujinx.Ava/UI/Controls/ApplicationContextMenu.axaml
+++ b/src/Ryujinx.Ava/UI/Controls/ApplicationContextMenu.axaml
@@ -67,7 +67,7 @@
     </MenuItem>
     <MenuItem Header="{locale:Locale GameListContextMenuExtractData}">
         <MenuItem
-            Click="ExtractApplicationLogo_Click"
+            Click="ExtractApplicationExeFs_Click"
             Header="{locale:Locale GameListContextMenuExtractDataExeFS}"
             ToolTip.Tip="{locale:Locale GameListContextMenuExtractDataExeFSToolTip}" />
         <MenuItem
@@ -75,7 +75,7 @@
             Header="{locale:Locale GameListContextMenuExtractDataRomFS}"
             ToolTip.Tip="{locale:Locale GameListContextMenuExtractDataRomFSToolTip}" />
         <MenuItem
-            Click="ExtractApplicationExeFs_Click"
+            Click="ExtractApplicationLogo_Click"
             Header="{locale:Locale GameListContextMenuExtractDataLogo}"
             ToolTip.Tip="{locale:Locale GameListContextMenuExtractDataLogoToolTip}" />
     </MenuItem>
diff --git a/src/Ryujinx.Ava/UI/Controls/ApplicationContextMenu.axaml.cs b/src/Ryujinx.Ava/UI/Controls/ApplicationContextMenu.axaml.cs
index fcae2ed38504..90c72e028921 100644
--- a/src/Ryujinx.Ava/UI/Controls/ApplicationContextMenu.axaml.cs
+++ b/src/Ryujinx.Ava/UI/Controls/ApplicationContextMenu.axaml.cs
@@ -289,13 +289,13 @@ public void OpenShaderCacheDirectory_Click(object sender, RoutedEventArgs args)
             }
         }
 
-        public async void ExtractApplicationLogo_Click(object sender, RoutedEventArgs args)
+        public async void ExtractApplicationExeFs_Click(object sender, RoutedEventArgs args)
         {
             var viewModel = (sender as MenuItem)?.DataContext as MainWindowViewModel;
 
             if (viewModel?.SelectedApplication != null)
             {
-                await ApplicationHelper.ExtractSection(NcaSectionType.Logo, viewModel.SelectedApplication.Path, viewModel.SelectedApplication.TitleName, viewModel.StorageProvider);
+                await ApplicationHelper.ExtractSection(NcaSectionType.Code, viewModel.SelectedApplication.Path, viewModel.SelectedApplication.TitleName);
             }
         }
 
@@ -305,17 +305,17 @@ public async void ExtractApplicationRomFs_Click(object sender, RoutedEventArgs a
 
             if (viewModel?.SelectedApplication != null)
             {
-                await ApplicationHelper.ExtractSection(NcaSectionType.Data, viewModel.SelectedApplication.Path, viewModel.SelectedApplication.TitleName, viewModel.StorageProvider);
+                await ApplicationHelper.ExtractSection(NcaSectionType.Data, viewModel.SelectedApplication.Path, viewModel.SelectedApplication.TitleName);
             }
         }
 
-        public async void ExtractApplicationExeFs_Click(object sender, RoutedEventArgs args)
+        public async void ExtractApplicationLogo_Click(object sender, RoutedEventArgs args)
         {
             var viewModel = (sender as MenuItem)?.DataContext as MainWindowViewModel;
 
             if (viewModel?.SelectedApplication != null)
             {
-                await ApplicationHelper.ExtractSection(NcaSectionType.Code, viewModel.SelectedApplication.Path, viewModel.SelectedApplication.TitleName, viewModel.StorageProvider);
+                await ApplicationHelper.ExtractSection(NcaSectionType.Logo, viewModel.SelectedApplication.Path, viewModel.SelectedApplication.TitleName);
             }
         }
     }
diff --git a/src/Ryujinx/Ui/Widgets/GameTableContextMenu.cs b/src/Ryujinx/Ui/Widgets/GameTableContextMenu.cs
index 6d8331658634..28ec5a43c753 100644
--- a/src/Ryujinx/Ui/Widgets/GameTableContextMenu.cs
+++ b/src/Ryujinx/Ui/Widgets/GameTableContextMenu.cs
@@ -270,8 +270,14 @@ private void ExtractSection(NcaSectionType ncaSectionType, int programIndex = 0)
 
                         int index = Nca.GetSectionIndexFromType(ncaSectionType, mainNca.Header.ContentType);
 
-                        IFileSystem ncaFileSystem = patchNca != null ? mainNca.OpenFileSystemWithPatch(patchNca, index, IntegrityCheckLevel.ErrorOnInvalid)
-                                                                     : mainNca.OpenFileSystem(index, IntegrityCheckLevel.ErrorOnInvalid);
+                        bool sectionExistsInPatch = false;
+                        if (patchNca != null)
+                        {
+                            sectionExistsInPatch = patchNca.CanOpenSection(index);
+                        }
+
+                        IFileSystem ncaFileSystem = sectionExistsInPatch ? mainNca.OpenFileSystemWithPatch(patchNca, index, IntegrityCheckLevel.ErrorOnInvalid)
+                                                                         : mainNca.OpenFileSystem(index, IntegrityCheckLevel.ErrorOnInvalid);
 
                         FileSystemClient fsClient = _horizonClient.Fs;