I'm culturing hiPSCs on matrigel, and these square shaped entities appeared in the center of the well plate. They don't move when plate is shaken, I'm not sure what this is.
I've seen many of those in my cell cultures when I add the medium to the cell culture too late, or even when the concentration of my growth factors was not balanced. You should reconsider what you are adding to your medium. Hope it helps :)