A three-dimensional simulation of a free-electron laser (FEL) with two beams is used to study the sensitivity of the third harmonic due to wiggler imperfections. In the two-beam FEL, for a fundamental wavelength of 107.5 nm, the power will be converted to the third harmonic at a shorter wavelength, in this case in the extreme ultraviolet at 35.8 nm. In this arrangement, the fundamental resonance of the higher energy beam coincides with the third harmonic of the lower energy beam, for this energy conversion to take place. For enhanced focusing, a planar wiggler with parabolic pole face is considered. Investigation of the effect of wiggler errors on the efficiencies of harmonic and fundamental resonance of the two-beam and the one-beam FEL shows that the average efficiency for the third harmonic in the two-beam FEL is decreased by 36% while the reduction of average efficiency for the fundamental of the two-beam is 55% and for the third harmonic of the one-beam is 48%. This shows that the third harmonic radiation in the two-beam FEL is less sensitive to wiggler imperfection compared to its fundamental as well as the third harmonic in the one-beam FEL. The reason is that the energy that transfers to the third harmonic of the two-beam FEL comes from both electron beams. It was also found that, for almost all cases, standard deviation increases with an increasing level of wiggler imperfection while, for the two-beam FEL, saturation length of the fundamental resonance decreases and the third harmonic increases with increasing wiggler imperfection.