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There is

More examples are given as answers to a similar question about problems NP-hard in $\mathbb R^3$ but not in $\mathbb R^2$:

  • Set-cover by half-spaces.
  • Finding a shortest path between two points among polygonal obstacles.
  • Determining whether a non-convex polygon/polyhedron can be triangulated without Steiner points.
  • Realizability problem for $d$-dimensional polytopes is a candidate ($d \leq 3$ vs $d \geq 4$).
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There is a similar question about problems NP-hard in $\mathbb R^3$ but not in $\mathbb R^2$.