When the Pentagon UFO tapes saw the light of the day some time ago, the press was eager to report on it and many speculated about alien life forms visiting us and other pseudo scientific nonsense. Without any regard to Occam's razor or to Paul M. Sutter's principle: "If it's interesting it's probably wrong!". Or to quote Fraser Cain of "Universe Today": "It's not aliens, it's never aliens!".
My best guess is, that it was a flock of seagulls.
The shots where there is one UFO to be seen, is most likely the parallax effect when traveling at high speeds and looking at an object at a great distance.
As the jet fighters were traveling at rather high speeds and the background being the ocean it makes this scenario very likely. It also explains the mysterious and supposedly fast moving object, that can be seen on the IR-camera. Since seagulls are masters at gliding it also explains why one does not see flapping wings.
To me the most likely scenario is, that it all started, when the pilots saw a flock of seagulls. At that point the birds were hunting fishes at one spot, causing the water to look like it was boiling due the many fishes and the dozens of birds getting them.
This strikes me as a very plausible explanation for the fact, that pilots reported a boiling spot of water of which the mysterious Tic Tac emerged.
Maybe a few of the seagulls were fleeing from the scene, because of the loud engine noises of the fighter jets. I am personally living at a place, where Panavia Tornados and Eurofighter Typhoons fly by on a regular basis and they are extremely loud despite not flying supersonic. In fact they can be so loud it makes normal conversations quite difficult at times. The fighter jets in the video are most likely FA/18 Hornets, which are quite comparable to the aforementioned planes. If those sounds are affecting me, it probably also effects the birds there.
So when the pilots applied their targeting cameras, they focused on one of the ducks and fell for an optical illusion.
While it is hard to believe, that trained pilots make mistakes, it certainly happens and with enough time and personnel spent on a task such as this, errors have to occur rather sooner than later.
Of course this whole post is highly speculative and I can not prove my thesis. However it displays an explanation for the footage and eyewitness report without resorting to highly unlikely occurrences such as physics violating aliens/aircraft.