ProTip:
Having now reviewed several save files for people, there are two common issues which can cause scenes to not seem to trigger with both having the same common cause.
"Speed Running" and "Console Editting"
tl;dr solution: Walk around for a bit, study, sleep, etc. Let the event scheduler catch up.
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RonChon has all of the events coded in a really neat way that actually helps avoid the issue of monkeying with things completely blocking the trigger from occurring from casual console abuse. The script which checks for events looks at the "Conditions" as well as the "Priority" of the event. Likewise, sequential events are gated by subsequent events checking the various history files.
(Example: "QuestPool.Quests['Jean Grey: Friendship'].completed")
So it is technically possible to break the game such that events won't progress from console, but you'd have to be deliberately attempting to do so with specific knowledge of exactly what values to enter.
However, if you have tried to speed run things via console, you are not going through the normal game play loop. Some also have day counts, so speed running in this case can specifically disrupt them..
Many of the conditions include specific time checks, who's present, etc. Since you aren't having to run to class, then head to the danger room, etc - you may not be actually hitting all of the conditional triggers when engaged in non-standard play. Likewise, you can have scenes which would trigger at the same time and thus when the event is selected only one of them can be.
In both cases you would need to give the event scheduler time to perform its routine checks (which occur throughout activites including when moving, sleeping, etc). Since some of these have different priorities it may take a little for all of these events to catch up.
