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This paper reports on the challenges and lessons we learned while running controlled experiments in crowdsourcing platforms. Crowdsourcing is becoming an attractive technique to engage a diverse and large pool of subjects in experimental research, allowing researchers to achieve levels of scale and completion times that would otherwise not be feasible in lab settings. However, the scale and flexibility comes at the cost of multiple and sometimes unknown sources of bias and confounding factors that arise from technical limitations of crowdsourcing platforms and from the challenges of running controlled experiments in the "wild". In this paper, we take our experience in running systematic evaluations of task design as a motivating example to explore, describe, and quantify the potential impact of running uncontrolled crowdsourcing experiments and derive possible coping strategies. Among the challenges identified, we can mention sampling bias, controlling the assignment of subjects to experimental conditions, learning effects, and reliability of crowdsourcing results. According to our empirical studies, the impact of potential biases and confounding factors can amount to a 38\% loss in the utility of the data collected in uncontrolled settings; and it can significantly change the outcome of experiments. These issues ultimately inspired us to implement CrowdHub, a system that sits on top of major crowdsourcing platforms and allows researchers and practitioners to run controlled crowdsourcing projects.