Manager Jim Vince pointed to a couple of refereeing decisions he saw as key to the reverse.
But the reality is that the Shaymen were caught cold for the home opener, scored by substitute Chris Almond with his first touch.
And they were given a mountain to climb when Tony Barras flicked out a leg to bring down the first goalscorer, Michael White firing home from the penalty spot.
Either side of the goals, Town had the bulk of the possession without ever really hurting Skelmersdale.
And, with the teams above them all having games in hand and better goal differences, it is that particular failing that could prove to be costly in the final reckoning.
As it is, a team that has struggled to score goals and to keep clean sheets is going to have to win its last four games for a chance to extend its campaign.
Skelmersdale had an early opportunity when Paul Evans was penalised, but Kevin Towey sent his free kick straight into the arms of Jon Kennedy.
Town's first chance came seven minutes later when Junior Brown played a great cross field pass for Michael Barnes whose cross was deflected behind for an Evans corner which was headed wide at the near post by Tony Barras
David Brown won another corner soon after, but home keeper Ryan McMahon claimed the kick comfortably.
The best bit of football in the first half came after 16 minutes when Tom Baker forced his way past three United players in the middle of the park before releasing David Brown.
The striker saw the keeper advancing and lifted the ball over him but wide of the target.
Baker fired a free kick straight at McMahon after Nathan Joynes had been brought down by Michael Akrigg before Skelmersdale squandered their best opportunity, Towey volleying an Aaron Turner cross straight at Kennedy.
Ritchie Sutton, a pre-game doubt with a tight hamstring, was forced to leave the field through injury on the half hour, but Town continued to enjoy the bulk of the possession without ever really threatening.
Junior Brown's through ball for Barnes was just too strong, Baker was unable to capitalise on a near post cross and David Brown forced a corner.
But not until the 45th minute did Town really have a shot in anger, Joynes turning well on the edge of the area before sending his effort over the bar.
The Shaymen started the second half well, creating a couple of chances, but McMahon was equal to both.
Joynes picked out strike partner David Brown who did well to wriggle through a crowd of players and get a shot in for the first.
And Baker and Evans combined well on the edge of the area before Peers fired in an effort for the second.
As so often happens, having looked like they were about to spark into life, the Shaymen went behind and it started after they had been on the attack, with Skelmersdale breaking swiftly down the left.
Tom Walker started the move before picking out Mark Houghton and his cross was met at the near post by Almond whose diving header gave Kennedy no chance.
Turner, lucky to be on the pitch for his assault on Junior Brown after he had already been cautioned, almost bagged another five minutes later but sliced his effort from 12 yards over the bar.
Skelmersdale did double their advantage with 10 minutes remaining from the penalty spot.
Michael White may have gone down theatrically, and the incident was close to the edge of the area, but Barras gave the home striker the chance to fall to the floor by sticking out a leg and White made no mistake from the spot, sending Kennedy the wrong way.
Town looked down and out, but still managed to make a game of it thanks to a mistake by McMahon who let a Peers 30-yarder slip through his fingers with less than two minutes remaining.
And that gave Town the chance to push forward one last time, Cavell Coo raiding down the right and sending over a deep cross which substitute Ashley Stott got up to head, but could not direct goalwards.

STAR SHAYMAN
As ever, Tom Baker was the driving force in midfield for the Shaymen with another energetic display.
His tackling was tough and he did what he could to drive the team forward.
Unfortunately his efforts went largely unrewarded on a disappointing afternoon to the team.
Baker's fellow midfielder Paul Evans was restored to the starting line-up and slotted straight back into his groove.
Accurate passing, good delivery from set pieces and an eye for the switch pass make him a real asset and he could be a key figure in the final four games if Town are to achieve their target of a top five finish.
Junior Brown was pressed into action as an emergency left back again following the departure through injury of Ritchie Sutton.
And while he is far happier - and better suited - to being further up the field, he did well in a losing cause.
Baker takes the three points on offer in our season long competition with Evans claiming two and Brown one.

MATCH FACTS
Skelmersdale Utd: McMahon, Foster, Crowder, Akrigg, White, Turner (Morrison 82), Towey (Walker 33), Wade, Houghton, Robinson (Almond 33), Armstrong. Subs (not used): Prescott, Duffy.
Booked: Turner 47
Sent-off: None
Goals: Almond 64, White 80pen

FC Halifax Town: Kennedy, Sutton (Peers 30), Coo, Adams, Barras, Evans, Baker, J Brown, Barnes (Stott 67), D Brown (Allen 77), Joynes. Subs (not used): Senior, Hinsley.
Booked: Baker (foul 32), Evans (foul 47)
Sent-off: None
Goal: Peers 89

Attendance: 588
Referee: P Davies

PLAYER POINTS
Tom Baker 41, Junior Brown 34, Ashley Stott 19, Scott Phelan 17, Jonathan Smith 16, Nigel Jemson 11, Paul Gedman 11, Colin Daniel 10, Peter Moore 10, Jon Kennedy 9, Cavell Coo 9, Paul Evans 8, Lincoln Adams 8, Damien Allen 7, Michael Barnes 6, Mark Peers 5, Ritchie Sutton 5, Adam Morning 4, Paul Collins 4, Luke Hinsley 3, Steve Payne 3, Neil Ross 3, Nathan Joynes 3, Craig Smith 2, Justin Walker 2, Craig Ellison 2, Danny Ellis 1, Phil Senior 1.

YOU SAY
We have enjoyed a good season really but today showed we are not good enough - BB

Time to go vince. Losin interest now. I wont be at shay again whilst were not gettin the right results - angry town fan

If mike tyson hit the deck as hard as baker he'd av bin asleep for a week. Tommy - a proper man straight back off the ropes ! team - nothing - Disappointed fan.

Dont stay 2 long vince ya 2 bit bum if it wasnt for tommy bakers spirit there wouldnt be anything of stature 10 feet tall mate god bless ya - shayman

Oh dear Shaymen - August, December, and February were really bad months for us - don't make April one - This division is to small for us - South Stander.
got to laff at a joke thanks for that lads good to see the skem fans found you a joke as well fact is you disgust me cheers - angry man

Not good enough shaymen. Plenty of effort but no quality up front. - Cath from Mytholmroyd

Mr Bosomworth, please sack Mr Vince and Mr Jemson NOW - shay andy

yet another tactical disaster jim. How many more times before you go? - ashamed town fan

the officials were as bad as towns pathetic attack - angry andy

36 games to get the balance & shape of the team right.You have failed badly Mr Vince.Junior Brown at left back. What a joke! Your inability to sign a quality striker has cost us a play off place - JRA.