Systematic errors are observed in dual comb spectroscopy when pulses from the two sources travel in a common fiber before interrogating the sample of interest. When sounding a molecular gas, these errors distort both the line shapes and retrieved concentrations. Simulations of dual comb interferograms based on a generalized nonlinear Schrodinger equation highlight two processes for these systematic errors. Self-phase modulation changes the spectral content of the field interrogating the molecular response but affects the recorded spectral baseline and absorption features differently, leading to line intensity errors. Cross-phase modulation modifies the relative inter-pulse delay, thus introducing interferogram sampling errors and creating a characteristic asymmetric distortion on spectral lines. Simulations capture the shape and amplitude of experimental errors which are around 0.1% on spectral transmittance residuals for 10 mW of total average power in 10 meters of common fiber, scaling up to above 0.6% for 20 mW and 60 m.