There was not necessarily any relationship between a will and burial record. However, it was incumbent upon the executor of a will to arrange the burial of the deceased. Often a testator would specify in his will where and how he would like to be buried.
There are several explanations, the most likely of which Dawn has mentioned - that he was simply buried elsewhere. Alternatively, the burial may have been inadvertently omitted from the register, the burial register may have been damaged or lost since the burial occured, or there may have been circumstances which prevented him from being buried in the churchyard.
Reading the will (and checking when/if/how it was proved) may shed some light on the mystery.
Alexander