With widespread adoption of Learning Management Systems (LMS) and other learning technology, large amounts of data--commonly known as trace data--are readily accessible to researchers. Trace data has been extensively used to calculate time that students spend on different learning activities--typically referred to as time-on-task. These measures are used to build predictive models of student learning in order to understand and improve learning processes. While time-on-task measures have been used in Learning Analytics research, the consequences of their use are not fully described or examined. This paper presents findings from two experiments regarding different time-on-task estimation methods and their influence on research findings. Based on modelling different student performance measures with popular statistical methods in two datasets (one online, one blended), our findings indicate that time-on-task estimation methods play an important role in shaping the final study results, particularly in online settings where the amount of interaction with LMS is typically higher. The primary goal of this paper is to raise awareness and initiate debate on the important issue of time-on-task estimation within the broader learning analytics community. Finally, the paper provides an overview of commonly adopted time-on-task estimation methods in educational and related research fields.