Airtight disappears and reappears randomly during the rescue mission for Sgt. Slaughter.
At one point, Hawk reads a report about the theft of Julius Caesar's ashes. He then says "Heaven knows what Cobra wants with them!" Well, if Hawk had been paying attention, he would know; moments before, Lifeline and Doc had just finished explaining Cobra's entire cloning scheme.
In part five, Bazooka is with the rescue team at the Terrodrome. Then it cuts back to Hawk talking to all the other Joes in the meet room of their base. As it pans over the audience, Bazooka is shown sitting in a seat. But a few moments later when the rescue team returns and walks in on them, Bazooka is back with them.
It is shown that Cobra found Montezuma's remains. Montezuma's body was destroyed sometime after his defeat and capture.
Some of the tombs shown raided are in the wrong location. Ivan the Terrible's tomb is shown as an isolated castle in northern Siberia, when in reality the Russian ruler's remains are buried in the Cathedral of the Archangel Michael near the center of Moscow. Also, Vlad Tepes is buried in the Snagov Monastery, located on a small river island near Bucharest, and not in Transylvania.
Several of the historical tombs mentioned as possible targets, historically do not in fact exist or have never been located. This includes the tombs of Sun Tzu, Genghis Khan. Alexander the Great, and Montezuma. Mention is also made of Julius Caesar's ashes, which are believed to have been lost centuries ago.
When Sgt. Slaugher shouts "Yo Joe! Let's stomp snake!" it is clearly the wrong voice.
There are 6 Devilfish and 8 SHARCs guarding Alexander the Great's tomb but only 3 of the former and 1 of the latter are seen battling Destro's forces.
Serpentor mentions that Cobra has troops stationed at the airport in DC. If this is the case, why do all of Cobra's planes end up having to retreat due to running out of fuel?
Briefly mentioned as one of the ancient conquerors whose DNA was stolen is Rasputin. Rasputin was in fact an eccentric Russian monk, and in his time was widely regarded as an eccentric mentally unstable man. His DNA would most likely be harmful to the DNA matrix of Serpentor, rather than of benefit.
Strato-Vipers change into regular Vipers during the battle with Sgt. Slaughter at Sun-Tzu's burial site.