I'm not sure why, but trigger explicitly a second GC collection fix the issue.

diff --git a/Python/pylifecycle.c b/Python/pylifecycle.c
index 2d5cb0ff78..d20ae01238 100644
--- a/Python/pylifecycle.c
+++ b/Python/pylifecycle.c
@@ -1295,6 +1295,7 @@ finalize_interp_clear(PyThreadState *tstate)
     /* Trigger a GC collection on subinterpreters*/
     if (!is_main_interp) {
         _PyGC_CollectNoFail();
+        _PyGC_CollectNoFail();
     }
 
     finalize_interp_types(tstate, is_main_interp);