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The massive amounts of web-mined parallel data often contain large amounts of noise. Semantic misalignment, as the primary source of the noise, poses a challenge for training machine translation systems. In this paper, we first introduce a process for simulating misalignment controlled by semantic similarity, which closely resembles misaligned sentences in real-world web-crawled corpora. Under our simulated misalignment noise settings, we quantitatively analyze its impact on machine translation and demonstrate the limited effectiveness of widely used pre-filters for noise detection. This underscores the necessity of more fine-grained ways to handle hard-to-detect misalignment noise. By analyzing the reliability of the model’s self-knowledge for distinguishing misaligned and clean data at the token level, we propose self-correction—an approach that gradually increases trust in the model’s self-knowledge to correct the supervision signal during training. Comprehensive experiments show that our method significantly improves translation performance both in the presence of simulated misalignment noise and when applied to real-world, noisy web-mined datasets, across a range of translation tasks.