Intensity correlation measurements of lasers oscillating in many transverse modes are found to be very sensitive to slight misalignment of the beams that have to be superimposed on each other for such measurements. This fact is shown to be due to the lack of spatial coherence in such lasers. It is theoretically shown that if the modes oscillate independently of each other, the fluctuation behavior becomes different for different points of the beam profile. This fact is demonstrated experimentally. An analysis of intensity correlation measurements of mode-locked lasers oscillating in many transverse modes is presented. The effects of slight mis-alignments on measurements of contrast ratios in two-photon fluorescence (TPF) patterns and second-harmonic measurements are discussed. In TPF measurements, even minute mis-alignments effectively reduce the contrast ratio from 3:1 to 2:1. Previously published data may be explained in this way.