The Coasters came unstuck early on as Boreham Wood scored their goals early and eventually went on to secure their place in the play-off semi-final.
Fylde missed out on a match with Sutton United as Wood won 2-1 on Thursday in front of the BT Sport cameras.
Challinor says the problems were of their own making and hinted things will have to change next season if they want promotion.
“We will look back over the next week or so and reflect on what we’ve done and where we have got to but ultimately it’s about now and we fell short,” he told us after.
“We have got to get back on the horse quickly to ensure we are in the correct state to be better next season and mount another challenge.
“We have done ridiculously well to get to where we have. When you get so close there is always going to be an overriding feeling of disappointment at not being able to finish the job.”
He added: “We had the opportunity to achieve something, we’ve not quite done it so we have got to move on and prepare to try again next season. We want to be in a good place come August next year and give ourselves the chance.
“We can’t fault the effort, but leadership and organisation at the back end of the pitch has cost us.
“They were two really, really poor goals we conceded in the first 20 minutes and it gave us a mountain to climb.”
“Credit to the player, we gave it a go but you can’t expect to score three goals in every match to win.