Unfortunately flaking at the cracks is a common problem with overlays. In cases where the floor is blemished and is needing an overlay we have found a better solution. Its called Metal Flake epoxy. (Pics attached) It comes in any color and has 10 times the durability and beauty of stained concrete. We offer it for $6 per sq ft and warranty materials and labor for 2 years. However, if your slab moves at the cracks enough it could crack also, but its not going to leave white flakes like your pictures show. The epoxy can cover the overlay avoiding the cost of removing it, and all the dust.
The other option is to polish the cracks back down to the slab and touch up the color, this leaves a visible crack with feathered overlay lines about 4-6 inches wide. Filling the cracks never lasts long and I believe will be money spent to a short term “band-aid”.