When Hernandez returned to Wellington yesterday he was approached by 3News at the airport but refused to comment.
Merrick told the Herald after last night's loss to the Mariners that Hernandez was sent home due to his injury and insisted there was no bad blood between the pair as he looked to Sunday's clash with Sydney FC in Wellington.
"He's had the thigh injury for about three weeks now. We thought he'd come good when we flew over but it wasn't good and the physio said `look, he can probably play one game' ... But he won't get through [two games in four days] so that was the decision made,'' Merrick said.
"We thought 'get him back, get him treatment and recover for Sunday'.''
Merrick did acknowledge there were concerns around when Hernandez's family would arrive in New Zealand but said the club were working through the required paperwork.
"He's definitely partly complaining about some issue with his family, which I don't really understand,'' Merrick said. "Our staff have been working really hard to help him get passports and visas and all the rest of it for his family and we are working through that so I don't actually know what's going on there.''
Phoenix general manager David Dome was overseas when contacted by the Herald last night and wasn't in a position to comment around the specifics of Hernandez's sudden return to Wellington.
Dome said it was club policy for a player to fly home from Australia on road trips if they were injured and unfit to play - Jason Hicks flew to Sydney yesterday to replace Hernandez - regardless of whether it was on the day of the game or not.
"We never leave a player when he's injured, we never leave him there,'' Dome said.
"Because it's much more expensive, you've got additional accommodation and food costs, all that sort of stuff and that adds up over time. So the policy is, if you're injured you just come back. Our strategy is, we don't take passengers ... You're either playing, or you're not playing.''
As for whether Hernandez was disgruntled around the delayed arrival of his family, Dome said he understood Hernandez's loved ones were due to arrive in New Zealand soon and believed there were no issues on the matter.
Dome said every player had a different agreement around their families and whether the club would foot the cost of relocating them to Wellington but said he didn't know the specifics of Hernandez's arrangement.