The former Swindon Town midfielder played for Arizona United SC for 45 minutes in a cup match.
However this was despite the Reds boss wanting him to be available for last Saturday’s home match against Plymouth Argyle.
Now it looks like his contract at Crawley will be cancelled unless a resolution can be made between Rooney and the club.
Manager Mark Yates said: “I don’t to waste my energy talking about him. He’s in America - I wasn’t happy about him going.
“I’d given him permission to go and then I had to take it back on the grounds that Jon Ashton was injured, Simon Walton was suspended, and we’d got a couple of other knocks.
“But he decided to go - that’s his bone of contention; he says he had written permission but I am the manager as far as I know and I’d asked him not to go, he went.
“He’s not in my plans. They want him to sign for Arizona United, if he wants me to let him sign for them and he wants to sign for them. Nothing will happen until that happens (giving permission).
“If not, he’ll be back Monday for training and we’ll take it from there.”
Rooney has struggled to hold down a starting place recently, and although he has made 22 appearances, that includes just nine starts in league matches, scoring one goal.
It is his second spell at Crawley having failed to make a start under Richie Barker during five months at the club in 2013.
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