Guimarães joined Arsenal in a £75 million transfer earlier this summer following protracted negotiations between the two clubs, during which Newcastle United rejected several offers before finally agreeing to sell the Brazilian midfielder.
He was a firm fan favourite on Tyneside, but reportedly pushed for the move once Arsenal's interest became known, leaving Newcastle to reluctantly sanction his exit.
"We did not want to lose Bruno Guimarães. That was really disappointing, that we got to that place in the end, albeit we were happy where we got to in terms of numbers," Wilson told Sky Sports.
"That was not part of our plan. Everything else that happened during the window was part of the plan."
Newcastle's summer also saw Sandro Tonali leave for Tottenham and Anthony Gordon depart, with the proceeds from all three sales reinvested in signings including Sean Steur, Lukas Hornicek, Amad Dedic and Nico Gonzalez as the club looked to reshape its squad while balancing the books.
The upheaval was compounded by Eddie Howe's surprise departure in August, fuelling a perception from outside the club that the window had descended into disarray, with the sporting director now tasked with steadying the ship alongside a new head coach.
Wilson pushed back firmly on that characterisation.
"Genuinely, it never felt chaotic inside. There is no point us pretending otherwise," he said. "That does not mean that every single player who signed was the number one name on our list, but that is never the case in any transfer window. Clearly we were disappointed a couple of times but, again, that's normal.
"No club goes into the window and reaches the end getting every target they set out to get. If they say they did, it is a lie."
He added that Newcastle considered their business for the season complete, though not necessarily final, leaving the door open for further incomings.
"We have built a squad for the season. That doesn't mean we might not make further alterations to it in January."