This is an issue that is present on 4.0.0 and 4.0.1, possibly others.
It occurs when "Retraction", "Wipe Nozzle", and "Perform retraction during wipe movement" are selected, and causes an overestimation.
The exact amount appears to be in relation to the total retraction distance for the print.
Example Part with 1.114 retractions;
0mm Retraction: 8056.1mm 23.40g (this one obviously has 0 retractions).
2mm Retraction: 12153.7mm 35.30g
6mm Retraction: 20854.5mm 60.57g
This issue can be partially mitigated by reducing "retraction distance", using "only retract when crossing open spaces" and "only wipe extruder for outer-most perimeters", and turning off "Force retract between layers". (Already off for my examples.)
Doing this for my example above with again a 2mm retract results in; 8753.3mm 25.42g
Opening the g.code with gcode.ws or running in on my printer shows that Simplify3D is producing the correct extrusion amounts and that only the statistics at the end of the file is incorrect.
I hope this was clear enough, and if any more details are required I'll be happy to provide them.