The problem appears after 6c627af3
('test: tarantoolctl: verify delayed box.cfg()'), where the test case
was changed and it doesn't more assume an error at the instance start.
So we need to stop it to prevent a situation when instances are stay
after `make test`.

Fixes #4600.
Reviewed-by: Vladislav Shpilevoy <v.shpilevoy@tarantool.org>

(cherry picked from commit 8d363c43)