Cover charge. Many izakaya serve a small starter called otoshi (お通し) that you did not order. It is charged per person, often a few hundred yen. This is normal and not a mistake.
Ordering. People usually order drinks first, then share dishes a few at a time.
Time limits. Busy shops may have a time limit, and the staff will call for a last order.
Standing bars. At tachinomi (立ち飲み) you drink standing up. They are cheap and made for a short stay. Some shops ask you to pay for each order.
Smoking. Some small bars still allow smoking, so check at the door if this matters to you.