Embryonic aneuploidy is highly complex, often leading to developmental arrest, implantation failure, and/or spontaneous miscarriage in both natural and assisted reproduction. Despite our knowledge of mitotic missegregation in somatic cells, the molecular pathways regulating chromosome fidelity during the error-prone cleavage-stage of mammalian preimplantation development remain largely undefined. Using bovine embryos and live-cell fluorescent imaging, we observed frequent micro-/multi-nucleation of missegregated chromosomes in initial divisions that persisted, re-fused with the primary nucleus, or formed a chromatin bridge with neighboring cells. A correlation between a lack of syngamy, multipolar cytokinesis, and uniparental genome segregation was also revealed and single-cell DNA-seq showed complex genotypes propagated by subsequent divisions. Depletion of the checkpoint protein, BUB1B/BUBR1, resulted in atypical cytokinesis, micro-/multi-nuclei formation, chaotic aneuploidy, and developmental arrest. This demonstrates that embryonic micronuclei sustain multiple fates, provides an explanation for blastomeres with uniparental origins, and substantiates defective BUB1B/BUBR1 signaling as a major contributor to mitotic aneuploidy.