Influenza A human isolates are rarely sequenced directly. Instead, a majority of these isolates (~70% in 2015) are first subjected to serial passaging for amplification, most commonly in non-human cell culture. Here, we find that this passaging leaves distinct signals of adaptation in the viral sequences, and it confounds evolutionary analyses of the viral sequences. We find distinct patterns of adaptation to generic (MDCK) and monkey cell culture. These patterns also dominate pooled data sets not separated by passaging type. By contrast, MDCK-SIAT1 passaged sequences seem mostly (but not entirely) free of passaging adaptations. Contrary to previous studies, we find that using only internal branches of the influenza phylogenetic trees is insufficient to correct for passaging artifacts. These artifacts can only be safely avoided by excluding passaged sequences entirely from subsequent analysis. We conclude that all future influenza evolutionary analyses must appropriately control for potentially confounding effects of passaging adaptations.