The altered logo also featured a Russian Sukhoi Su-57 fighter jet and a triangular-shaped aerial vehicle, all flying over a map of the United States.
The flying saucer was first noticed by a UFO enthusiast who posted about it on Twitter.
He wrote: "UFO in the official seal? Hahahhahaha. Radical. I still can't believe they did this."
A spokesman later made clear it had not been intentional.
US intelligence has shifted its approach to UAPs, with the phenomena being taken more seriously.
The report to Congress in 2021 concluded that the vast majority of sightings by US military personnel could not be explained.
However. it said in many cases the UAPs were real objects because they had been picked up by multiple sensors.
Highly advanced aircraft
The report was unable to rule out the possibility some of them could be highly advanced aircraft operated by foreign adversaries.
Pentagon researchers reviewed 144 sightings but said only one of them could be confidently explained.
The report was delivered to the House and Senate intelligence committees by Avril Haines, Joe Biden's director of national intelligence.
While the report was released publicly a classified annex was made available only to US senators, which led conspiracy theorists to speculate about what was in it.