Yes, it has happened that some US votes have not been tabulated, and where this is known, not even retabulated.
For example, consider the 11/22/2000 "Brooks Brothers Riot", that many believe had, (one way or another), a decisive effect on the 2000 US Presidential Election, wherein a small organized horde of posturing, domineering, middle-age Republican paid zealots were deployed to bully and delay Miami-Dade canvassers attempting to recount the 10,750 remaining poorly-designed ballots that their elections computer was unable to tally.
The riot, planned by the notorious Roger Stone, and ably orchestrated out of a nearby winnebago made into an impromptu wireless command center, made it impossible for the frightened canvassers to complete the recount prior to the deadline of 11/26/2000 set by the Florida Supreme Court. So the 10,750 ballots were not counted as votes.
Three weeks later, voting on partisan lines, the United States Supreme Court mooted the Florida Supreme Court's recount order, but nobody really knows if those 10,750 Miami-Dade ballots had been tallied, and if, (since Miami-Dade usually votes Democrat), the resulting votes had put Gore to win Florida, as to whether or not the resulting changes in public opinion might have inclined the Supreme Court to demur.