Well, the reason for that is because there were two Best Actress envelopes. One was in Emma Stone's possession, while the other was mistakenly given to Mr. Beatty.
PricewaterCoopers, the accounting firm that oversees the envelopes, now explains that two of their reps, Martha Ruiz and Brian Cullinan, were stationed on both sides of the stage. Both also had their own briefcase containing envelopes of all the winners.
Ruiz handed off the Best Actress envelope when it was time to announce the award, the penultimate of the night, and then immediately following that, when Best Picture was about to be announced, Cullinan also handed off his duplicate of the Best Actress envelope. OOPS!!!