As the other guys said. It almost certainly points to beatgrids that aren’t right.
Once you’ve initially analysed the tracks in Engine DJ desktop you can reanalyse them to get a deeper algorithm with more accuracy.
How to do that is simple. Eject any song in the onscreen deck, go to your main collection and CTL-A then right-click. You’ll see reanalyse in this menu. This uses a deep analysis and does not just give you a grid based on BPM like the initial scan.