I understand your scenario. But you don't understand mine.
Let me try with some more specifications. We are concerned with the gravitational field at the position (1,0,0). We position a sphere of radius 1 at the origin (0,0,0). Our point of interest is at the outer edge of this sphere. The gravitational field of this sphere at (1,0,0) points in the negative x direction, yes?
OK, now we have to add up the gravitational effect of everything else. Now consider a spherical shell around our original sphere, of inner radius 1 and outer radius 2, still centered at the origin. Our point of interest is on the inside of this sphere. Shell theorem applies, the net field at (1,0,0) from this surrounding shell is zero, yes?
So we keep going. Now we make a shell of inner radius 2 and outer radius 3, still centered at (0,0,0). No field at (1,0,0). And so on, and so on. Of course we need an infinite sum of such shells, but that's OK, because the contribution of each shell is always zero. And so I've proven that the gravitational field at (1,0,0) is pointing in the -x direction.
But I could redo the same proof starting with a sphere and concentric shells centered at (2,0,0), and I would prove that the gravitational field at (1,0,0) is pointing in the +x direction. In fact, I can pick spheres to come up with any magnitude answer and pointing in any direction I want. This is a paradox. You cannot resolve it by appealing to the shell theorem, since that's part of how we got in this mess. You can't resolve it by saying the shell theorem is invalid, because it's mathematically rigorous. And you can't resolve it with your calculation method, because that's just one of many equally valid ways to calculate the answer. There
is an explanation for why this paradox arises, but you have to go beyond the shell theorem to understand it.
ETA: and spheres and shells aren't even the only way to do this. You can also use infinite slabs with finite thickness (which is easy to solve analytically and produce finite fields), and the same thing applies: you can arrange the problem to get whatever answer you want.