Castle Living Space Anomaly

The Castle Living Space Anomaly, often shortened to CLSA, is an uncommon occurrence within Super Mario 64 that can drastically change the interior of any castle of the game, even anomalous ones such as The Sunken Castle. These changes usually add furniture to the castle to make it feel more lively, rarely even removing paintings altogether. It is noted that the total star count of any copy with this anomaly is usually much lower than the average copy.

The anomaly tends to "favor" anomalous or alternate castles, though it isn't too rare to find the vanilla castle affected by the changes. Regardless of which castle it is, rooms are often repurposed to fit much more basic needs, such as one of the painting rooms getting turned into a kitchen or the basement becoming a proper basement. Rarely, however, rooms can outright vanish to make more space for other things like a guest room.

The Wing Cap Anomaly
The Wing Cap Anomaly is an anomalous phenomenon that appears to only affect copies that are also under the Castle Living Space Anomaly. This is a secondary effect wherein the "Tower of The Wing Cap" stage, and associated Wing Cap, is almost always removed or replaced in some form. This is usually due to the castle interior changing in a way such that the standard method of entry is no longer possible.

In it's place, the A.I often implements other anomalous Power-Ups, including The Yellow Cap Switch, Rainbow Cap Switch, Fire Flower, and in rarer cases Gold Mario. Courses are usually not changed to reflect this, however, so certain Stars may become impossible to collect with intended gameplay.

Theories
It's possible that the castle was always meant to have furniture, but simply got removed in favor of a freer environment. It's also worth nothing that Nintendo has suggested that the Princess has two castles- one for paintings, and one for furniture. Ergo, this anomaly was probably just leftover code for a second castle that may have went unused, which would potentially explain why the anomaly "favors" anomalous or alternative lobbies.

As for the Wing Cap Anomaly, some have thought that whatever CLSA was intended for was meant to provide new challenges and new Power-Ups, so the Wing Cap gets axed to make room for these powerups. It is uncertain why the Wing Cap is chosen in this case.