Just got off my first Nekton Cruise -- Pilot in Medio this week. I've been on Blackbeards, Aggressor, Juliet and Paradise Charters -- so I've seen other ops. Op is a bit frayed around the edges. You get what you pay for. Crew smokes a lot. Reality of "We request that you depart the boat by 9:30am on the day of return" translated to 3 crew members knocking on our door at 8:00am saying: "We NEED you aff the boat NOW." Thanks for coming, eh? Feel the love.
Departure times were always a problem for us in Ft. Lauderdale (at least they were after 911). The boat makes a reservation with U.S. Customs and Immigration for a set time in the morning, but sometimes the officers arrive very early and they are unwilling to wait for passengers and crew to go through the process of showing their passports and collecting the paperwork. These officers also require that all luggage be in the salon when they arrive for possible inspection. Other times the officers show up late which causes even more problems, as we have had guests almost miss their flights because Customs/immigration does not show up until 11:00ish and people have planes to catch.
I was not there, so I can't speak for what actually happened (and it seems a little more tact on the part of the crew was warranted), but my guess was that this was more the fault of US Customs and Immigration than it was of the company.