No, verified audit trails do not increase the likelihood of malfunctioning, because malfunctioning is often caused cheating. Having audit trails make cheating less likely, because having audit trails makes it more likely that cheating will be caught. With an audit trail, voters can make sure that their vote is properly recorded for the right candidate.
Voter verified paper audit trails do not increase the likelihood of an electronic voting machine malfunctioning. While the paper may comfort a voter, it is not an effective check for malfunction unless a significant number of people would return with the paper and report their concerns. Additionally, some people who are disabled are not able to use the paper which would be unfair.