The teenage pair worked with Stoke's academy director Steve Holland at Gresty Road but he has dismissed any suggestions of foul play.
Holland told the Sentinel: "I want to clarify that Ben and Matthew turned down contracts at Crewe.
"I received a phone call from both players asking if Stoke would be interested in signing them. Then I had a conversation with Dario Gradi at Crewe to inform him of the situation.
"It's possibly a situation that will now develop when the players return from their holidays, but it's not a foregone conclusion or a done deal."
Stoke will have to pay compensation for the duo if they sign.