I’m having a small problem having two series of squares and inset circles to correctly loft together. They look fine at first, but upon closer examination it seems the wrong control points are connected, hence the very visible crease lines. On a vertical profile, what should appear is like a slightly rising volcano profile, instead it looks like a suction cup. Hope that makes sense. Thanks in advance!

Your curves are not internalized so the definition is useless. The usual issue with lofting circles to other curves is that circles are degree 2 curves with low point count. Use fit curve on the circles to degree 3. Then it should be fine. Also, make sure seams are aligned.