Make sure you haven't used too much thermal paste, too much will isolate the heat, which will give higher temperatures. The pea-sized dot in the middle of the CPU is the easiest and best way, in my opinion, to to put on thermal paste. The heatsink will spread the thermal paste for you.
Also make sure the stock cooler's pins is all the way through your MOBO.
Stock coolers is highly dependent on air flow, so if you have a case with bad air flow then it might be an issue as well.