Wolverhampton Wanderers boss Gary O'Neil has confirmed that Jonny is currently not available for selection due to a "training ground incident".
With Wolves missing Craig Dawson, Rayan Ait-Nouri, Mario Lemina and Joao Gomes for Saturday's Premier League fixture at Arsenal, the versatile defender had been expected to feature on the substitutes' bench.
However, Jonny was a notable absentee from the squad, subsequently leading to question marks over why he did not make the trip to the Emirates Stadium.
A report in the Express & Star claimed that his omission was due to an incident at the training ground in the days leading up to the previous match.
With Wolves playing host to Burnley on Tuesday evening, O'Neil faced the media on Monday where he was naturally quizzed on the situation.
Although O'Neil opted against going into detail, he acknowledged that the report was correct and that the long-serving Spaniard would not be selected for the foreseeable future.
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O'Neil said: "Jonny won't be in the squad tomorrow. There was a training ground incident last week that's being dealt with by the club.
"If and when he's back available we'll let everyone know. At this moment he won't be available for the coming games. I'd rather not go into details in public, the club is dealing with it."
The 29-year-old has already endured a frustrating campaign, being restricted to two starts in the EFL Cup and just four minutes of Premier League football.
Jonny had been available for transfer during the summer transfer window, but Wolves did not receive a suitable offer and the Spain international was happy to fight for his place at Molineux.
During a stint that has been impacted by two serious knee injuries, Jonny has made 134 appearances for Wolves since initially arriving on loan in 2018.
With just 19 months remaining on his contract, the expectation is that the former Celta Vigo man will again be available for transfer in January.