The colt was bought by Godolphin after winning the Vintage Stakes at Glorious Goodwood, where he took his unbeaten record to three.
However, the son of Dream Ahead never looked comfortable at any stage at Town Moor and trailed home last of the six runners.
“He’s been unsound since he ran at Doncaster and he’s on his way to the Newmarket Equine Hospital for a bone scan,” said Johnston on Thursday afternoon.
“It looks like he’s got a stress fracture of his pelvis or higher up.
“He’d still be top of the tree of my two-year-olds.”