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I experience this in the Sun Temple, when grazed by a bat during a fall(which triggers the being hit animation) and landing on a blue platform while the animation is still active.
This paralyses the player char.
I can still navigate menus, but the character won't move until I forcefully quit the game and start it up again.
This bug is also referenced on Steam:
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I'm afraid this post isn't going to help you at all...
That said I think that this is clearly a bug harcoded in the Linux port of the game: since the source code isn't open, I'm afraid that only the developer can do something to fix it, but it probably won't.
As said in the Steam's thread, the only solution seems to be switching at least temporarily to the Windows version of the game, running it via Wine.