I've only worked with epithelial cell lines, but whenever I would see yellow clusters like this, my cells were growing in colonies and overconfluent in the centre of the colony. I assumed these yellow spots were cells dying and being extruded from the plate. I would recommend seeding at a lower density or making sure you mix the cells well before plating so they don't clump up and start dying.

Natalie Ronaghan Thank you for your answer. Yes, I resuspend them well before plating and then shake plate up-down, left-right. Never in a circle. Most of the plates are great, no yellow spots and even higher density of desired cells, but still sometimes something like this happens.

Perhaps something is growing along with your cells? Looks like they are aggregates of some sort of fine bacilli-like structures...and not all cells have them. A quick solution would be to simply throw these cells away, thoroughly clean the incubator, hood etc and start with fresh cell stocks from some other batch. Another approach (if you really want to find out and have time and materials at hand) would be to carry out some sort of viability assay on cells after they are infested with these structures. If you get high viability results in comparison to some "cleaner" cells of the same cell line, then this is some contamination. If these are dying cells, you shouldn't see higher viability. You do have debris but debris doesn't just piggyback onto adherent cells....

Vidhya V Iyer thanks for the advice. I kept on growing them and they look better now. I am trying to wash them thoroughly even after primal removal of feeder cells.