The Taiwanese opposition has called for a recount and an independent inquiry into irregularities in the election. These are some key areas of concern.
Claims that Mr Chen engineered the shooting to win sympathy votes.
Taiwan's military was put on round-the-clock combat readiness status after the assassination attempt, preventing soldiers from voting.
There was an unusually high number of spoiled ballots.
Video footage taken at a polling station in Chiayi county showed a girl stamping and casting a ballot for an elderly voter.
968 votes cast for the opposition in Kaohsiung were allegedly miscounted as votes for DPP candidates, while 428 votes for DPP candidates were reportedly counted for the opposition alliance.
Some ballot boxes for presidential and referendum votes were opened at the same time, violating election rules.
When three voters in Kaohsiung went to get their ballots, they were told they had already been used.