In routine experimental operations, 96-well deep well plates are frequently used basic consumables, widely applied in various experimental scenarios such as sample storage, reagent preparation, extraction and purification, and reaction incubation. Featuring neatly arranged wells and compatibility with batch operations, they serve as core tools for bulk sample processing. However, in daily practice, many researchers operate based on established habits and overlook detailed specifications, leading to frequent errors. These seemingly minor operational mistakes often result in sample contamination, reagent waste, biased experimental data, sample loss and other issues. They not only raise experimental costs but also delay the overall experimental progress. Combined with long-term practical experience, this article summarizes 5 typical errors most commonly encountered in daily use, elaborates on the hazards and corresponding correct operation methods, to help researchers standardize operations and avoid mistakes.