We have encountered the very rare occasion where the inclusionChecker is following very closely with the log/shard tree-head and happens to miss an included certificate. Re-starting ct-woodpecker with the LogIndex set back a couple tens of thousands allows ct-woodpecker to "see" the certificate it missed, and then continue on as normal.
I don't yet know how it could have missed the certificate it submitted, only that ct-woodpecker at the time was very up-to-date, following the shard's tree-head quite closely (ct-woodpecker itself may have been the only entity submitting to this shard).