It is implied that Andy Woodward fell out with Neil Warnock, but Warnock actually signed him for Sheffield United in 2000, although he only made three appearances due to injury.
Barry Bennell talks about Woodward being let go by Halifax when he goes to see him in prison, but this had nothing to do with his performances on the pitch as implied here, it was due to the fact that the club went bust in the summer of 2002.
In the opening scene Neil Warnock is shown as Manager of Bury in 1997. He was Manager of Oldham Athletic in 1997. He didn't become Bury Manager until the summer of 1998 and was Manager until December 1999 when he took over at Sheffield United.
The opening dressing room scene with Neil Warnock ranting at his players is based on a real event, including the famous line "you, you're in Lativa" at a player, but this actually happened when he was Manager of Huddersfield in April 1995 against Shrewsbury Town not at Bury as shown here, it also took place at half-time in real-life not at the end of the game as portrayed here.