The scene of Jedi's landing on Naboo on TF transports which was implicitly shown in the movie could not take place under any circumstances. That's because in order to reduce the manufacture costs and to make easier the maintenance, the ships designed for inert cargos (which were used by the TF for landing the droids on Naboo's surface) were not airtight, had no heating or other life support systems and could not be used to transport living beings.
A few hours after the Jedi landed the landing of the TF forces started. Since by the will of the Force and Chance the pod fell close to one of the large "gugny" refining facility, encountering the gungans, as well as the TF forces became all but inevitable.
Unlike in the film, the rescue of Jar Jar Binks (a partisan-deserter out of Boss Nass' force) included no exchange of fire with the droids, which would have inevitably exposed the Jedi to the TF. Jar Jar was knocked down by a droid's swoop bike and the hiding Jedi saw him to be in the path of a TF crawler (not nearly all the TF battle machines were fitted with repulsors, as for the technology shown in the movie, at the time of the "wet war" the majority of it was non-existent yet). Using the Force, the Jedi pulled Binks under their cover, thus saving him from an inevitable death or injury.
The scene of negotiations with Boss Nass as shown in the movie is largely veracious except for a few details. For example, it's obvious that even the careless gungans had to maintain a black-out during a war, and their underwater domes at the times fad no force field walls but were made of natural materials (stripes of certain reptiles' hardened saliva). Jar Jar Binks' exile "for idiocy" also replaced the death sentence for deserting the battlefield, to which he was sentenced shortly before the events described in the film. The circumstances of this are unclear, as well as his discharge and elevation before the battle with the main TF forces.
The "bongo" travel shown in the film is for entertainment alone. According to all the sources available to us it was a boring and tiring sailing which lasted 1.6 standard (Coruscant) days.
The scene of releasing queen Amidala and organizing her escape from Naboo is shown quite correctly, except that actually over a half of the guards escorting the queen were injured or killed on the way to the hangars.
The scene of breaking through the blockade is shown amazingly close to the true events. At least, all the existing memoirs of the witnesses describe it exactly the same and in exact accordance to the film. The only doubts are about the scene of honoring R2-D2, probably inserted in the film to enhance the catharsis.