The only problems with microchipping I've heard of is, they can move from the original location and some studies have shown a slightly increased risk for developing tumors at the injection site. Other studies have shown this is not true.....kind of like cell phones and brain cancer...you don't know who or what to believe.
I prefer tattooing over the microchip. With a tattoo the identification is seen immediately and you don't have to have the lost pet scanned. And, there are registries for tattooed pets.