The Fill tool works by first identifying all the sinks in the input raster that satisfy the specified z-limit, then replacing the cell value of the identified sinks with the lowest value in the adjacent cells. It is important to note that the z-limit only influences the selection of the sinks to be filled, not their fill value. Situations where sinks are adjacent to other sinks provide an opportunity for the filled value to exceed the z-limit, because the lowest adjacent value can come from another sink that was filled using its lowest adjacent value.
For example, assume sink #1 is surrounded by sinks from all sides (sinks #2 through 9). Each of the adjacent sinks will inherit the lowest possible value from their surrounding sinks. Sink #1 will then inherit the lowest possible value from the filled sinks surrounding it, thereby making it possible for the difference between the filled cell's resulting value and its original value to exceed the specified z-limit.
The following graphic further illustrates this scenario:
The profile graph at the bottom is of the original elevation model; whereas, the profile graph at the top is of the Fill output. The Fill tool was executed on the elevation model with a z-limit of 5, and the symbolized display is the result of subtracting the original surface from the Fill output.
All the filled values that exceeded the z-limit are either partially or fully surrounded by other sinks.