Just speculating wildly (would like to see a definitive answer with links, maybe you can post the paper link this came from?)
IIRC the ribosome pauses awaiting the next tRNA then ratchets forward a codon at a time. Maybe when they are captured for Ribo-Seq they are mostly in a paused state (e.g. mostly positioned relative to a codon). So maybe this is reflective of that iterative ratcheting process, and it's completely normal?