For the disk space, it can be a bit tricky sometimes. There are actually two conditions (below certain MB threshold AND below certain % threshold) that have to be met at the same time for the alert to fire. Great concept, as it tries to accommodate for disks of different sizes, but this also happens in missing an alert sometimes which is probably what happened here. You can choose to have to satisfy only one condition if you want, disable the default monitor and enable only the criteria you want (MB or %).
As for the server down alert, do you know if the server was back up within a few minutes? That can cause SCOM to not fire alert as the missing heartbeat is taken into account after 180 sec (default) of downtime. If the server was down for longer than that, see if any override was in place.