Does anyone now why slic3r is flipping my object when printing? If you look at the gcode view it’s correct but when it’s printing it prints it flipped?
You got one endstop in the wrong side
Direction is wrong. Flip the end stop homing direction and flip your motor wire 180 deg.
@MakerGal @Griffin_Paquette it only does it with this part.
Are you printing on a Cartesian or linear Delta printer?
@Douglas_Pearless its a Cartesian machine if you’re facing the printer all the endstops are to the left it’s a cubepro that I open sourced.
left and back?? or left and front??
@MakerGal left back
everything its correct. You try different slicing softwares??
Your origin should be in the front left corner of the platform. Sounds like your Y axis is reversed.
Its there already, he has the end stops in the left and the back. aso it get the origin in the front-left corner
Ok that means you typically have the wiring for the X axis stepper motor reversed, ( or the Y axis depending on the orientation of your print job 
) simply unplug the motor and rotate the connector 180 degrees reversed. Make sure you change of the endstop as well otherwise it will crash into then end when you HOME as it will now go in the opposite direct.
@Whosa_whatsis Yes the origin is in the left front corner.
And you say @jacob_keller that only mirror that piece?? are you shure?? You print more pieces with that machine?
@MakerGal The cubepro uses the old BFB-3000 frame with a different plastic case over it. The important fact to know about this machine for this purpose is that it moves the extruder in X and Y. Mendel-style machines have their Y endstop in the back because they move the platform in Y instead of the head. All motion should be considered motion of the tool relative to the platform, even if the platform is moving, so moving the platform to the back is better thought of as moving the tool forward. When the platform is moving, the endstop needs to be in the back because that’s where the platform will be when the head is at the front, but if the head is moving in Y, the Y endstop needs to be in the front.
Ooooh yes yes @Whosa_whatsis , it similar to a Core XY construction, yes the endstops should be in the front and left
@MakerGal @Whosa_whatsis @Douglas_Pearless this is what I have. It came from the factory like this.
missing/deleted image from Google+
But like that, you got Y axis Inverted, as @Whosa_whatsis said, with that constrution your endstop should make that the nozzle when homing stops in the left-front coner. As you got your nozzle stops in the left-back corner, so the machine will mirror your pieces around Y axis
@MakerGal I’ll change the y Axis then. Thanks for the help.