What I suspect is happening is that the “matching” polygons in adjacent frames have differing numbers of vertices and/or the “matching” vertices aren’t in the same order, and so the transition engine we have tries to transition between two polygons that aren’t particularly similar to each other, geometrically, and does its best, which is what we see here.
For example if I have a triangle ABC transitioning to a square DEFG (assuming that geometrically A is “near” G and B is “near” D and C is “near” E without necessarily being in the same place, like maybe the square and triangle are slightly translated/rotated):
A GF
BC DE
then the “matching” points A and D aren’t in the same place, and there’s a new point G that has to come from somewhere, so you’ll see a really rough transition. In general there’s not a straightforward algo that I know of for arranging these things with minimal ugliness.
The problem is compounded by the fact that you’ve got a covering set of polygons, but the transition oddities between adjacent polygons aren’t correlated, so you get this odd effect 