This causes no problem whatsoever, it's just good to keep some hygiene over ignored files. Add generated Flatpak files and folders to .gitignore.
@@ -99,3 +99,10 @@ tags
.DS_Store
*/.DS_Store
*/**/.DS_Store
+
+#flatpak
+/.flatpak-builder/
+/_flatpak_build/
+/flatpak_app/
+/repo/
+/CI/flatpak/flatpak-github-action-modified-*