that is because the heat retention of the plastic is high and that part of your part overheats (you input more heat into it then it is able to dissipate itself due to head being too long in too small area) ... there are number of ways to solve this
- increase cooling when "layer time" is lower then some amount
- slow down print speed when "layer time" is lower then some amount
- print "multiple copies" of same part allowing head to go to a different part of bed and spend time there (printing other copies) allowing part to cool enough
- print scrap object (prime pillar often used for this..) (uses less plastic then printing 2 pieces when you need only one)
...
S3D have decent support for this (check out cooling tab), you can manually up the fan for those layers, you can let it use "fan override", also speed tab, there's "speed overrides" for small layers...
p.s. the "size" of the layer is determined by "time to print layer" or "layer time" .. I for e.g. call any layer faster then 30 sec a "problematic" one

and I allow speed reduction, as for the fan (even for ABS!) I don't let it "fan override" (as I don't really know what exactly s3d does there and I didn't bothered to make few tests and figure out) but I manually set fan speed for layers where I want it (it's fast and easy)
gcodestat integrates with Simplify3D and allow you to
Calculate print time accurately (acceleration, max speed, junction deviation all taken into consideration)
Embed M117 codes into G-Code
Upload your G-Code directly to Octoprint
open source and unlicence