Quality of datasets plays an important role in large language model (LLM) alignment. In collecting human feedback, however, preference flipping is ubiquitous and causes corruption in data annotation; the issue necessitates the alignment algorithms with improved robustness against potential flipped pairs. To this end, this paper introduces a Flipping-Aware Direct Preference Optimization (FA-DPO) algorithm tailored to preference flipping from a reinforcement learning with human feedback (RLHF) perspective. We dissect the inherent human intention model and the preference flipping mechanism introduced by external factors as two distinct stages; in the latter, we introduce an instance-dependent flipping probability on the basis of the Bradley-Terry (BT) model. Further, by leveraging features relevant to preference annotation, we capture uncertainty in judgments and model preference flipping patterns. In practice, we design a simple yet efficient iterative optimization algorithm compatible with the original RLHF and DPO algorithms. In our experiments, we investigate the instance-dependent preference flipping model under multiple circumstances for evaluation of our proposed method, as well as other baseline methods. The model implementation details and the code, as well as a complete manuscript with colored hyperlinks and technical appendix for better digital viewing, are included as supplementary materials and scheduled to be open-sourced upon publication.