Module analysis for multiple-choice responses (MAMCR) was applied to a large sample of Force Concept Inventory (FCI) pretest and post-test responses (N_pre = 4509 and N_post = 4716) to replicate the results of the original MAMCR study and to understand the origins of the gender differences reported in a previous study of this dataset. When the results of MAMCR could not be replicated, a modification of the method was introduced, modified module analysis (MMA). MMA was productive in understanding the structure of the incorrect answers in the FCI, identifying 9 groups of incorrect answers on the pretest and 11 groups on the post-test. These groups, in most cases, could be mapped on to common misconceptions used by the authors of the FCI to create distractors for the instrument. Of these incorrect answer groups, 6 of the pretest groups and 8 of the post-test groups were the same for men and women. Two of the male-only pretest groups disappeared with instruction while the third male-only pretest group was identified for both men and women postinstruction. Three of the groups identified for both men and women on the post-test were not present for either on the pretest. The rest of the identified incorrect answer groups did not represent misconceptions, but were rather related to the blocked structure of some FCI items where multiple items are related to a common stem. The groups identified had little relation to the gender unfair items previously identified for this dataset, and therefore, differences in the structure of student misconceptions between men and women cannot explain the gender differences reported for the FCI.