It has lead the Barack Obama campaign to seek a court order to keep the polls open after hours.
Several of those precincts with ballot shortages were around the U.C. Berkeley campus, which Obama supporters had expected would favor them. Alameda County says no candidate was robbed of votes.
The Obama campaign isn't convinced, but says there may be nothing that can be done about the ballot shortage. However, they are considering all options regarding the so-called bubble trouble in Los Angeles.
"L.A. County has 12 million people. This could literally be thousands of tens of thousands," says Steve Westly, California Obama Campaign.
Voters who were given Democratic ballots in Los Angeles County needed to mark a bubble selecting the Democratic party. If they failed to do that, the machine would not count that ballot.
"We want to make sure that we don't disenfranchise anyone and every vote is counted and we want to move quickly to make sure that it is reconciled," says Dean Logan, Los Angeles Co.
Steve Westly says it's premature to talk about a lawsuit. Los Angeles election officials say they will review the ballots.