Poor PA announcements - from poor quality, overlapping, volume issues etc
Inconsistent application of baggage rules - 4 women in a row going through with a handbag and a roller suitcase but the Mrs being informed its a 1 bag limit and she has to leave the queue to put her handbag in the suitcase (which she then takes back out as soon as she passes the attendant)
Security at the gate rather than after check-in - makes liquid limits both harder to apply and slower
Long queues, sometimes mixed up with other flights when gates are close, to be "first on" when the airline operates a phased basis. Separate lines for each phase, fully distinct from other flights are much better.
Lack of announcements when somethings gone wrong... worst case was on an Air France flight once where they'd cancelled our 6:20am flight the night before due to predicted bad weather, on the day it happened to be good weather. When arriving at 4:20am and the board said delayed and to go to Cust Service which didnt open until 8am and so nearly 4 hours stood in a queue to a closed desk.