Large language models (LLMs) are increasingly prevalent in security research. Their unique characteristics, however, introduce challenges that undermine established paradigms of reproducibility, rigor, and evaluation. Prior work has identified common pitfalls in traditional machine learning research, but these studies predate the advent of LLMs. In this paper, we identify nine common pitfalls that have become (more) relevant with the emergence of LLMs and that can compromise the validity of research involving them. These pitfalls span the entire computation process, from data collection, pre-training, and fine-tuning to prompting and evaluation. We assess the prevalence of these pitfalls across all 72 peer-reviewed papers published at leading Security and Software Engineering venues between 2023 and 2024. We find that every paper contains at least one pitfall, and each pitfall appears in multiple papers. Yet only 15.7% of the present pitfalls were explicitly discussed, suggesting that the majority remain unrecognized. To understand their practical impact, we conduct four empirical case studies showing how individual pitfalls can mislead evaluation, inflate performance, or impair reproducibility. Based on our findings, we offer actionable guidelines to support the community in future work.

Large language models trained on web-scale data can memorize private or sensitive knowledge, raising significant privacy risks. Although some unlearning methods mitigate these risks, they remain vulnerable to "relearning" during subsequent training, allowing a substantial portion of forgotten knowledge to resurface. In this paper, we show that widely used unlearning methods cause shallow alignment: instead of faithfully erasing target knowledge, they generate spurious unlearning neurons that amplify negative influence to hide it. To overcome this limitation, we introduce Ssiuu, a new class of unlearning methods that employs attribution-guided regularization to prevent spurious negative influence and faithfully remove target knowledge. Experimental results confirm that our method reliably erases target knowledge and outperforms strong baselines across two practical retraining scenarios: (1) adversarial injection of private data, and (2) benign attack using an instruction-following benchmark. Our findings highlight the necessity of robust and faithful unlearning methods for safe deployment of language models.