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At the end of Captain America: The First Avenger we see Howard Stark's team recover the Tesseract from the ocean floor.

in Captain Marvel we learn that the power source to the Lightspeed Engine Mar Vell was developing was the Tesseract found in Mar Vell's lab which was a Kree Impiral Cruiser in orbit of Earth.

Since Howard Stark was a founding Member of S.H.I.E.L.D after Captain America: The First Avenger S.H.I.E.L.D has the Tesseract, but given Fury was detained when looking into Project Pegasus (what Mar Vell was working on) this means Project Pegasus wasn't a S.H.I.E.L.D project.

So how did S.H.I.E.L.D lose ownership the Tesseract to Mar Vell?

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At the start of The Avengers, the place where the experimentation is ongoing on the Tesseract under the guidance of Erik Selvig, is Project Pegasus.

This is the name of the project that was being led by Mar-Vell on Earth in the 90s.

SHIELD never lost the item, they handed it off to Project Pegasus for research. It's possible that Mar-Vell recognised it for what it was and removed it (as lead scientist she would have that capability) to her hidden lab.

Goose eventually returns it to Fury in Captain Marvel's end credit scene

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