We can only speculate, but from what i have read about the hack, many people are suspecting this to be what happened, it was probably an inside job, maybe someone in their team added something malicious to their code, but until Atomic Wallet tells us what happened, we can only speculate, that's why closed source wallets aren't good.
Newbies should not only stay away from Atomic Wallet, but all closed source wallets, like Trust Wallet, the victims this time is users of Atomic Wallet, but who knows the closed source wallet that is next.