When McGarrett and Johnny Noah are put in jail, they are still wearing their belts and their neckties. Under standard police procedure, when a person is booked into a jail, those items would have been confiscated.
In the interrogation room at the jail, attorney Sid Kane starts a fire in the trash can. No alarms go off, no police officers respond to the smell of smoke.
McGarrett is arrested, booked into jail, then released on his own recognizance. In the next scene, he enters a house with his gun drawn, accompanied by other police officers. If he was out on bail, he would have been suspended from his job, and not allowed to possess a firearm.
Lee tried to get into Johnny's car as the latter was leaving his apartment building's garage, tossing the attache case into the back seat, but was pulled away from the car by some bouncer type working nearby. So Johnny left with this cash, and Lee did not shut the car door, yet when it turned right to get out of the garage, the door was shut.
The photos used to frame McGarrett were obviously not taken from the person on the gangplank. They were taken onboard the boat.
When McGarrett drives himself and Gloria (Zohra Lampert) to a meeting with Johnny Noah (Richard Romanus), just before he exits his car, the sound crew and their equipment are clearly reflected in the shiny paint on the driver's side of the vehicle.
When Steve drives to the meeting with Johnny, he passes over two arrows indicating he's travelling in the wrong direction.