The La Liga club had agreed a deal in the region of £7m to sign Fornals, who is keen too return to his homeland after falling down the pecking order at West Ham.
Fornals, who joined West Ham three-and-a-half years ago from Villarreal, has failed to score or register an assist in 11 starts and 12 substitute outings for the Hammers across all competitions this season.
The 27-year-old was in attendance for West Ham's 1-1 Premier League draw with Bournemouth at the London Stadium on Thursday night and was pictured pacing up and down the tunnel on his phone waiting to discover whether his transfer to Betis would be given the green light.
However, the deal is yet to be confirmed and Fornals remains a West Ham player for the time being, as IT issues from the English club's end have put the deal on the brink of collapse.
Despite this, Betis chief Alarcon remains "optimistic" that the deal can be finalised and hopes it will all be resolves in the coming days.
"There was a last-minute problem with Fornals, we think it was a computer problem," Alarcon told Spanish reporters.
"Betis sent all the documents correctly and on time and it seems West Ham had a computer problem. It wasn't just with Betis it was with other deals. We hope that it gets resolved in the next few days.
"It was done on both sides. We imagine that with a computer error it can be resolved. We are working on it and we are optimistic."
Meanwhile, West Ham manager David Moyes issued a fresh update on Fornals's situation at a press conference on Friday, and he remains hopeful that the midfielder can secure his move to Betis.
"I think there is a chance the Pablo deal will be ratified. I can't confirm if it will or it not at the moment though," Moyes told reporters.
There was more drama at West Ham on deadline day as Said Benrahma's proposed move to Lyon fell through at the 11th hour, and the Ligue 1 club have since slammed the "incomprehensible behaviour" and "lack of respect" by the Hammers in their efforts to get the deal done.
Lyon had agreed to sign Benrahma on an initial loan deal until the end of the season with an obligation to buy in the summer for around £15m.
FIFA have reportedly launched an investigation to discover why West Ham failed to part ways with both Benrahma and Fornals in the final few hours of deadline day.