He bemoaned his men not taking their chances while lauding second-placed league campaigners Rangers doing just that, although both sides butchered goals.
The Rovers went up 1-0 in the 10th minute from a penalty to midfielder Ryan Tinsley after referee Matt Stone adjudged Miramar midfielder Cole Peverley to have handled the ball in the 18m box amid howls of protest.
However, Miramar struck back, 1-1, in the 25th minute through striker Tom Jackson whose electric pace on the right flank left centreback Finlay Milne hamstrung and defensive midfielder Rob Pearson somewhat out of sorts.
But it was Rangers 2-1 up in the 59th minute when captain Patrick Fleming fed off substitute Richard Bott's educated switch-play cross to score after a Blues' blunder on attack.
Tinsley again stepped for an equalising penalty to make it 2-all in the 81st minute to the delight of the parochial fans and dismay of the Miramar stable.
But it was homeboy Andy Bevin, in a visiting strip, who tipped the scales in the 86th minute for a 3-2 lead when Pearson's misdirected header from a long-range ball beat his fellow defenders.
The OK Corral-type exchanges continued with Tom Biss levelling 3-all to push the game into extra time.
A minute before the first half of extra time expired, an adroit player who once brought unfathomable joy to the ground over the years this time inflicted pain on a hushed crowd when Bevin latched on to a Fleming long ball to chip a golfing wedge-like shot over a charging goalkeeper, Kyle Baxter, to seal victory.
"It is what it is and we're obviously paying for it," said Wilson, reflecting on a winter of injuries and unavailabilities but loath to take anything away from a gallant Miramar who defied odds to inflict the first loss on the Blues on home soil this season.
He said the Rovers still had a cup to defend in the league and the O'Brien Challenge Shield to retain at home with the Rangers to return on July 24.
The Blues play Wairarapa United next away this Sunday and host Petone on July 10.
"Just like Bill said, we'll be hurting for a few days but we'll be back on track next week to get three points."
A relieved Miramar coach, Wiremu Patrick, agreed it was a game befitting a cup final but ...
"I don't think it's everything I'd want in a cup match but it was awesome, mate, and we enjoyed it and it could have been a cup final," Patrick said with a laugh.
He felt his men needed to learn how to close out games when they are leading but acknowledged both sides were guilty of not converting chances.
"They'll obviously be disappointed but we're just going to move on from it."
Patrick refrained from criticising officials but revealed his players made contact with the ball in both the penalties although he reconciled that with "sometimes they go [your way] and sometimes they don't".
"When you come to a place like this and walk away with a win you've got be happy."
He agreed Bevin had "mixed emotions" but praised him for his pride in helping the collective, adding he replaced him in extra time because he was cramping.
It was Bott's injection that opened up the game but a jovial Patrick laughed when asked if he would start him in their next game although he felt it was a reflection of the depth in their squad.
