It is widely recognized that we need to prepare students to think with data. This study investigates student interactions with digital data graphs and seeks to identify what might prompt them to shift toward using their graphs as thinking tools in the authentic activity of doing science. Drawing from video screencast data of three small groups engaged in sensor‐based and computer simulation‐based experiments in high school physics classes, exploratory qualitative methods are used to identify the student interactions with their graphs and what appeared to prompt shifts in those interactions. Analysis of the groups, one from a 9th grade class and two from 11th/12th grade combined classes, revealed that unexpected data patterns and graphical anomalies sometimes, but not always, preceded deeper engagement with the graphs. When shifts toward deeper engagement did occur, transcripts revealed that the students perceived the graphical patterns to be misaligned with the actions they had taken to produce those data. Misalignments between the physical, digital, and conceptual worlds of the investigations played an important role in these episodes, appearing to motivate students to revise either their experimental procedures or their conceptions of the phenomena being explored. If real‐time graphs can help foster a sense in students that there should be alignments between their data production and data representations, it is suggested that pedagogy leverage this as a way to support deeper student engagement with graphs.