"runs" or "sessions" in Structural MRI - Purpose and Implications for Quality Control
It is common to remove especially motion-corrupted MRI runs without excluding the subject.
Without more knowledge about the project it's hard to know why exactly they have multiple runs present and whether there are differences between runs or just repeated scans. It may be that the operators made sure to collect more data when they suspected subjects had too much motion during the scan, they may have done so randomly or by convenience (such as according to patient comfort), or they may have had other reasons.
I would consult other papers published using the same data set (even the functional ones) for their inclusion criteria.