The reverse transcription-polymerase chain reaction (RT-PCR) test to detect SARS-CoV-2, the virus causing COVID-19, has been regarded as the diagnostic gold standard. However, the excessive sensitivity of RT-PCR may cause false-positive outcomes from contamination. Again, its technical complexity increases the chances of false-negatives due to pre-analytical and analytical errors. This narrative review explores the elements contributing to inaccurate results during the COVID-19 pandemic and offers strategies to minimize these errors. False-positive results may occur due to specimen contamination, non-specific primer binding, residual viral RNA, and false-negatives, which may arise from improper sampling, timing, labeling, storage, low viral loads, mutations, and faulty test kits. Proposed mitigation strategies to enhance the accuracy of RT-PCR testing include comprehensive staff training in specimen collection, optimizing the timing of tests, analyzing multiple gene targets, incorporating clinical findings, workflow automation, and implementing stringent contamination control measures. Identifying and rectifying sources of error in RT-PCR diagnosis through quality control and standardized protocols is imperative for ensuring quality patient care and effective epidemic control.