At one point, a search for the energy of the Tesseract turns up traces of five similar artefacts on Earth. While the reader is aware by this point that the only other Infinity Stone on Earth is the Time Stone, considering that the odds of two Stones being on the same planet by chance must be considerably small, it’s possible that all six Stones were on Earth at some point before being sent elsewhere and the search just picked up traces of the Stones’ energies.
Granted, Tony is later able to confirm that the other Stones aren’t on Earth in the present and even identify their present spatial locations, but considering that the Time Stone is kept secret by the Masters of the Mystic Arts it’s not unreasonable to assume the order were able to set up a ‘fake’ trail for the Time Stone’s location.
