A conscious decision has been made to make some important and frequently used structures mutable - meaning that they are modified in place, rather than being immutable.
These classes are mutable to reduce memory churn and use, as otherwise every operation would result in a new object being instantiated into memory. This becomes clear in physics and collision calculations, allowing for more memory efficient operations to be used, rather than creating a large number of objects into memory just to discard them at the next garbage collection.
This is not only important for keeping memory use down; but more importantly reducing the time the garbage collector requires to clear out objects - this garbage collection event is handled by the browser, and is beyond the control of the engine or the game. The garbage collection event is blocking, and will occur between frames; if it takes too long it could lead to stuttering behaviour and game freezes.
These key structures are mutable in the engine: