On IRCTC till 20 July or so 3A and 3E are clubbed together for bookings so if you book a ticket in 3A till that date you may be allotted a berth in 3A or 3E by the algorithm and will have to pay full 3A fare. If you get allotted a berth in 3E then the difference of fare will get refunded back to your account or card depending on how you made the payment.