The Time-Picker is now always being displayed since updating to the latest 4.9.3 release of Meta-Box. A second time-picker will pop up when the time entry field is clicked on as expected, but there is now a second time-picker widget that is permanently displayed on the page.
To recreate this issue simply place a cloneable group time element like so:
array( 'name' => __('Event Time','tevents'), 'desc' => __('Time before countdown launch to trigger this event.','tminus'), 'id' => $prefix . 'event_time', 'class' => 'tminus_time_toggle', 'type' => 'time', 'js_options' => array( 'timeFormat' => 'HH:mm:ss', 'showSecond' => true, ), )