Everything that's organically decomposing generates heat, it's part of the process and further accelerates the process.
May I ask what prompted you to stick a themometer in an apple? Also you might want to try some vegetables too (I have always imagined a turnip would be relatively warm).
could also be the pressure of shoving a thermometer into an apple "squeezing" the base, thus causing the "mercury" (probably red colored water) to rise.