It probably means you have another patch enabled that has modified the same code:
Code:
#
# The following three patches are mutually incompatible,
# don't enable more than one.
#
# `ePub fixed/adjustable top/bottom margins`
# `ePub fixed top/bottom margins`
# `ePub disable built-in body padding-bottom`
#
The first two patches include the effect of the `ePub disable built-in body padding-bottom` patch, so there is no need for it if you are using one of the other two.