The observation of exoplanets during their primary transits and secondary eclipses is a powerful tool to characterise their atmospheres. These observations provide important information about their temperature structures and circulation efficiencies, as well as the ability to detect the presence of clouds, hazes and specific molecular features. However, repeat observations of hot Jupiters routinely yield significantly different results. Without understanding the source of each of these disagreements, which could arise due to systematic errors or genuine atmospheric variability in the exoplanets themselves, it is difficult to reliably constrain the atmospheric properties of these exoplanets. I will present a summary of these discrepancies—including my own secondary eclipse observations of WASP-12b—along with a discussion of their various causes. I will also describe future ground-based and space-based observational strategies to discriminate between explanations involving storms and systematics.