There could be several explanations for this.
FutureproofedCities assumes that a measure starts out at full speed as from year 1 and that the evolution of a measure progresses in a linear fashion. If your climate plan works at cruising speeds (i.e. it takes a few years for the measure to hit full speed), then the results during your measure could be different.
If there is a gap of a few years between the reference year and the start of your climate plan, it could be that a reduction has already been implemented concerning your reference year, while your climate plan still has to be initiated. This reduction is usually attributable to policy efforts at a higher level (Flemish, Federal, European), general trends, lower emission factors, etc. It is logical that your total reduction is consequently higher than the reduction from your climate action plan.