Logan has tended to be short on return agents in the late afternoon for the past couple years - I'm usually returning cars around 5 for a flight a little after 6, so I'll just leave the keys and go. They tried to charge me an extra day once based on the time they finally got around to checking it in, 6 or so hours later, rather than when I dropped it off. I sent them a copy of my boarding pass showing my flight out of BOS was before my required return time and they reversed it. I've also had occasional problems with them charging fuel because I'm a few miles under the threshold where they'll automatically charge fuel unless you show them a receipt. When I drop the car and go now I always take a geotagged/timestamped picture of the odometer, the fuel gauge, and my fuel receipt before I get out of the car.

Probably because 2/3 of the cars already smell like someone smoked in them and they were poorly cleaned. I've had my share of cars that smelled like poorly cleaned post-smoker rentals but fortunately they've never tried to charge me the cleaning fee.