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When Mystique shape-shifts, she looks like the person she wants to imitate with their clothes on.
Now, if she removes these clothes and puts them away and then returns to her original form, do the clothes stay there? If so, isn't she violating one of the fundamental laws of physics, that something can't be created from nothing?
I suspect her upgrade was less about making objects and more about turning her into a more malleable and hopefully interesting living weapon. If I were a responsible writer, I would try and keep such transformations into objects into short term events. Or just create a material she could transform in the same fashion as she does her cellular structure.
This required an analysis of her powers and eventually a correction to their description:
Her cellular structure was far more malleable than believed since she could make metal where our bodies did not have nearly as much metal available at the cellular level.
She was not just transforming her cells, she was transforming matter at a limited level.
She had been seen converting metals from her clothing into weapons. It was not disclosed whether that was a special technology or a power she kept hidden until then.
In 2001's X-Men Forever miniseries, Mystique is exposed to dangerous levels of radiation in order to save the life of Toad. The process morphs Mystique's appearance to match her more reptilian physique from the 2000s film trilogy, and boosts her powers so that she can now morph her body into taking certain desired physical traits depending on her situation at the time.
With her revised powers (a classic Marvel "Radiation Accident") her transformations now include powers such as night vision, wings on her back, talons in her fingers, and natural body armor. These powers make more sense since she would be getting them by imitating things already seen in nature. A cat-like eye would have better night vision, for example.
She can even compress nearly two-dimensional like a sheet of paper to glide on air currents, similar to Mister Fantastic, which she uses to survive an explosion. She has moved her vital organs out of place in order to survive a gunshot to her torso. This is a bit more of a stretch (pardon the pun) but since matter transformation has been shown, the writers decided to go ahead and utilize it in a limited fashion, giving the character more durability and flexibility in combat.
She has, once with strain, given herself two heads and four arms to facilitate a gun fight on two fronts, as well as shapeshifted into herself as a small child. She is also now able to hold a shape when knocked unconscious and can conceal items in shapeshifted pouches under her skin.
This was clearly the case of a character whose powers were poorly defined and allowed her to do things that were not explained well (where did her clothes come from, how did she take them off, where did the metal in her clothing come from, why didn't she have the power to transform into shapes other than human, why didn't she get any special abilities, etc) and "corrected" during a movie tie-in. This made the character appear physically the same as her movie version and allowed writers to try and clean up and stabilize a power suite that would allow her to keep up with the diverse powers of the X-men.
