The Cod Army have now won just one of their last seven games and lie six points adrift of the play-off places following their third defeat in four away matches.
Pilley publicly criticised the team after the game but said Graham Alexander's position as manager is not in danger.
He said: "Far from happy with that, lots of players not up to standard.
"One way or another we will be better. I hate losing, not being messed around by certain people any more.
"We look after staff exceptionally well, certain deluded individuals should remember that before it's too late for them."
He added: "My issues are not with GA (Alexander), he is doing an excellent job."