In her previous scenes we see that Bubble is practically impervious to any physical damage as she can alter her body so she won't get hit or damaged.
So what happened to Bubble in her last scene?
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The official novelisation indicates that she was repeatedly stabbed while defending Valerian. There's no special indication that, even as a shapeshifter, her body is capable of taking that kind of damage.
The fact that the guards didn’t appear to have much in the way of armor—well, much in the way of any kind of clothing, really—made it that much easier. They did know how to use their weapons, but he seemed to be quick enough to dodge them without any harm.
The fight… Valerian had fought like a madman, certain that the blades wielded by the guards weren’t even touching him because he was just that good. Of course the weapons hadn’t struck him—Bubble had protected him with her own body, taking blows meant for him. He hadn’t even thought about her—he was too busy being headstrong, impulsive Valerian. And now—