I actually followed a few steps and checked my printer's calibration. It was really good. It almost takes the same amount of filament that I wanted to extrude (set to 100 mm and measured 100.21 after extrusion). Followed the instruction here:https://www.youtube.com/watch?v=YUPfBJz3I6Y

Quote Originally Posted by flatty_420 View Post
There is a bearing on the front of the extruder (mounted opposite the hobbed gear) that you can watch and see very easily what the extruder motor is doing.

I did check if the extruder does retraction and it does. I can even see the what the motor is doing as flatty_420 described.

I have been watching as it prints and as I said before, when it starts a new layer -at the very beginning of the new layer- the extruder extrudes just a little bit of more filament than it usually does and I guess that is why it causes this problem. (I also measured my filament and it was always around 1.75-1.74-1.76 so averaging it changed nothing).