United tried to sign both Baines and midfielder Marouane Fellaini, but had to settle for only the Belgian midfielder.
"The way the transfer deadline goes, everyone looks at it and it got to a stage where we knew the Gareth Bale (to Real Madrid) thing was going to happen," Stubbs told The Sun.
"That was the big one. Underlying from that, there wasn't really an awful lot going on.
"Probably come seven o'clock on the night (September 2) at Everton the word from the training ground was that no one was going to go.
"Fellaini was staying. Bainesy was never really an option - the club had dug its heels in. Bainesy had obviously said he'd like to go.
"And then, come nine o'clock, suddenly we started to get linked with Lukaku and then the Fellaini thing was starting with negotiations with United. By the time it had finished we'd bought three in and they are great additions to the squad."