A recovery transaction is OMNY's attempt to recover an earlier fare that was not collected successfully. They have a policy referred to as "tap tap go" that allows riders through after two unsuccessful tap attempts. This is so they don't leave riders stranded due to connectivity issues with the bank or issuer, but it creates a negative balance on the rider's OMNY account.
The next time the person rides the train, their first tap results in a recovery transaction that collects the negative balance. They are asked to tap a second time, and the second tap results in a new charge for the current ride. If the rider presents a new form of payment after the first tap, the new form of payment receives the charge for the current ride.
Sometimes the recovery transactions happen as part of a batch cycle, often overnight. And that is why some riders report charges happening while they're sleeping.
The charges are legitimate and tied to earlier rides that you may not have been charged for. You can contact OMNY to understand which rides the recovery transactions are associated with.