This study investigated undergraduate students metacognitive judgments while learning about complex science topics using multimedia material (text and graph). A within-subjects design was used to examine the effect of discrepancies on study-time allocation, metacognative judgments and inference generation. There were three types of discrepancies: none, text (between two ideas in the text) and text and graph (between the text and graph). Forty (N=40) participants completed 12 trials where they were asked to provide 6 judgments: Ease of Learning judgments (EOLs), immediate and delayed Judgments of Learning (JOLs) for both text and graph and Retrospective Confidence Judgments (RCJs). Participants provided significantly lower JOLs for content that contained discrepancies but RCJs remained high across conditions. Discrepancies did not influence study-time allocation, but did significantly influence inference scores. Overall, results suggest that participants may be aware of discrepancies, but lack the control strategies needed to overcome them.