Problem with spring force in growth algorithm

From visual inspection, a guess: your upper shape “grows” by splitting two joined faces into four faces by adding a center point to their shared edge, then extruding that point for all four faces.

Yet it looks like your lower image isn’t geometrically the same. It appears to have geometry like skin tags – a group of faces held on to the main body by a single shared edge. If you were using a divide algorithm like above, that should be impossible.