Factual error: When the Marines strip off and run into the sea in the final scene, Doc takes off a pair of white socks that would be more appropriate for a final at Wimbledon. Not only are they white rather than khaki, they are virtually spotlessly clean which would be impossible after a week of fighting on the black sands of Iwo Jima.
Continuity mistake: When the "Flag-Raisers" begin stripping down to go swimming, they show a few of the Marines already down to their boxers. They switch to a shot of Bradley and then back to the Marines and all have their pants on.
Continuity mistake: When the marines start marching inland, where the Japanese are not shooting, you see several clips of the row of soldiers walking inland, then a clip of their waiting comrades, and then a clip of the soldiers - still walking in the exact same place, without moving forward.
Deliberate mistake: During the scene on the train in lounge car, a picture on the wall prominently shows an ALCO PA locomotive. The movie was set in 1945, but this locomotive was first produced in 1947.
Continuity mistake: When Ira exits the stadium after the flag show to vomit, the alleyway in which he vomits is at first dark. In the next few shots, it is lit up and then once again dark.
Revealing mistake: There are several scenes (most notably when the group is ambushed at Mt. Suribachi) where the bayonets attached to the guns bend back and forth showing them to actually be rubber instead of metal.
Audio problem: When Rene Gagnon is playing the guitar on the ship his hand movements do not match the guitar that is playing.
Other mistake: During the hill climb up terrain shaped like a valley with rocks on either side, a soldier is directly hit with a large explosive, probably from the big guns, and his severed head lands down on another soldier's back, who is crouching to help another man. When the head lands on his back, it is just an empty helmet, but when he looks at it on the ground, you see the partially alive, severed head lying next to it with much of the neck still attached.
Continuity mistake: When Ira is leaving Chicago on the train, the train starts moving while he's standing and saying goodbye the last time. In the next clip he's shown right next to the train door, but that would have moved further away.
Continuity mistake: The monument was dedicated in November 1954, but Rene Gagnon (and Ira Hayes for that matter) didn't look one day older during the ceremony than during the battle 10 years earlier.
Factual error: The water is perfectly still around the ships as they bombard the island. When the cannons fires there are small ripples on the water from the shockwave, but around the ship it remains perfectly calm.
Answer: The movie insinuates that he was killed horribly but doesn't provide many details. Books about Iwo Jima have quotes from witnesses about what happened to him and they all say that he was very brutally tortured, including having his eyes cut out and his genitals removed and stuffed in his mouth. The book "Flags of Our Fathers" contains the following quote, "A few days later someone yelled that they'd found him. They called me over because I was a corpsman. The Japanese had pulled him underground and tortured him. His fingernails... his tongue... It was terrible. I've tried hard to forget all this.