I don't believe this is directly covered anywhere, but they change shape frequently.
The Tesseract manifests as a cube in our reality. Space Stone
The Aether is a liquid that can exist within a personsperson's body. Reality Stone
Loki's sceptre has a gem on it but a different shape to the final gem. It also conveniently fits into Vision's forehead receptacle. Mind Stone
The Soul Stone looks the correct shape but is too big before Thanos claims it.
The Time Stone and Power Stone look around the right shape and size already.
They seemsseem to conform to the expectations of those wielding them, Thanos needs them to fit in his glove so they do.
