The Self-Patching Anomaly

In some personalized copies of Super Mario 64, glitches such as the Backwards Long Jump, Cloning, and ways to reach Parallel Universes cannot be done by any means, or odd quirks revolving around them seemed to be patched out. This can be theorized to be caused by what is dubbed as "The Self-Patching Anomaly". This anomaly can seem to decrease the amount of glitches that can be done. Regional differences in what glitches can be done can also be caused by this anomaly, as the base game for it to be personalized in it of itself would be based on a personalized copy of it. It’s similar to the Shindou Build of Super Mario 64, Since it patched the Backwards Long Jump in that build.

The anomaly itself also has an opposite effect, as some copies of the game had failed to "self-patch" via this anomaly, causing newer glitches to occur. Sometimes, it can render a save of the game or an entire copy of Super Mario 64 to be unusable due to these new glitches. Other times, it can be a backdoor for other types of personalization to occur. No one has documented newer glitches.

Different saves of one cartridge can have different types of glitches to be patched or added.

Theories
The Self-Patching Anomaly's development is currently unknown at this point. There are two possible theories that were derived from this ambiguity; that this anomaly was a way to hide the personalization from the public eye, or that it was used as a way for the game to self-patch itself without developers needing to do the work to add it to the game.

The first theory states that since some personalization mechanisms could lead to malicious effects, this anomaly was produced so that Nintendo could lessen the chances of these factors to occur so that they don't face repercussions. This goes off the idea that Super Mario 64 itself is a creation that's malicious in it of itself, which can be seen in some people's point of view and that Nintendo is shady and mysterious when it comes to the personalization of the game.

The other theory sets the tone that this anomaly wasn't made for malicious intent, as it could be a way for the developers to reduce time fixing bugs when the personalization AI can do it itself. Since a lot was scrapped from the game (it was stated that 32 levels were supposed to be made from the game), time seemed to be a huge issue for production of it. As such, this anomaly could have been set in by the developers of Super Mario 64 so that more progress can be made working on the other contents of the game before it hit the deadline.