depending on how the plotter is setup the y axis has a problem,...if it was setup to cut as most do the y axis is the knife carriage direction and the x axis is the direction the grit wheel rollers move the roll of vinyl,....on most plotters the knife carriage y axis is set by sensors on the knife carriage that read the position of the pinch wheels,...my money is on the fact you may have knocked one of the pinch wheels out of a specified area to area that will give the plotter an error reading,..thus if you check and make sure the pinch wheels are within the specified area or move them so they are,... you may very well eliminate your problem,....
edited to add,... if the plotter is setup to read the movement of the vinyl on the grit wheels to be the y axis( in the direction of the roll of vinyl) the sensors are usually photo cells(small hole with glass cover) on the platen(base that the cutting strip is on and the vinyl rides over) this can be corrected as previously stated by covering the hole with some opaque tape or vinyl