Assuming that K is smooth or locally flat, there is a nice geometric reason based on transversality.

The Klein bottle is not orientable.  If it embedded in R3 so as to separate a small epsilon neighborhood of its image, then the neighborhood would be homeomorphic to a trivial line bundle over the Klein bottle, K times (-1,1), and therefore the neighborhood would also be non-orientable.  But since any 3-dimensional submanifold of R3 is orientable this cannnot happen.

So the Klein bottle embedding would have to be non separating in this neighborhood.  But this means there is a curve C in the neighborhood that intersects the embedded Klein bottle once, transversally.

Now C bounds a disk D in R3 since R3 is simply connected. (Bounding any surface is enough).
One can make D transverse to the Klein bottle K, leaving boundary D fixed. One then see that K intersects D in a union of arcs and closed curves, with a single boundary point.  But any such collection has an even number of boundary points, a contradiction.

This argument works more generally to show a closed nonorientable surface cannot be embedded in a 3-manifold M with H1(M;Z2) = 0.