Do you mean the difference between the core temps and the "CPU temp" listed with your motherboard software?
The core temps are just that. Sensors in each core. The CPU temp is the temp in the case of the CPU. This will always be cooler.
NONE of these sensors report an actual temp. They report movement in temperature, and it's up to the software to interpret the raw data into meaningful numbers. So different software can say different things.
Core Temp, Real Temp, HWMonitor and Speedfan are the programs that are most used and usually agree on temps.