Merrick said Sigmund's injury was a contributing factor to the loss as the visitor's defence was exposed by Sydney's Italian star Alessandro Del Piero, who scored two first-half goals from a penalty and free kick.
A reflective Merrick spoke glowingly of his crop of inexperienced players but noted work was needed on the defensive flanks and in midfield.
Blenheim–born Sigmund and some of his teammates who also play for New Zealand's national side have recently come in for criticism from former All White Fred de Jong, a Sky Sports New Zealand commentator but also the boss of the NZ Football's High Performance program.
But Merrick wasn't having a bar of that.
"I've always been happy with the boys that have backed up for both the All Whites and then come and played for the Phoenix and given 100 percent," Merrick said.
"Ben Sigmund played with a torn thigh (tonight) so that's another player out injury-wise and Andrew Durante had a terrific game but that's only two in the back line.
"I thought our fullbacks (Michael Boxall and Shaun Timmins) struggled a bit tonight.
"I feel as though we only have one midfielder defensively at the moment and that's Vince Lia," the coach added.
"I think young Matt (Ridenton) is a good prospect but not good defensively, Kenny Cunningham couldn't get in the game and Carlos was very good for going forward but he has never been great for defending and our defensive midfield really exposed our backline.
Merrick surmised the three-goal loss wasn't a total disaster despite the fact it put the final nail in the coffin of the side's finals prospects.
"I thought we started the game well, we looked good," he said.
"(We) knocked it around and created some good chances and we don't have that hardened mentality when things go against you, when decisions go against you and goals go against you.
"The bottom line is you can't ever compete unless you are turning that possession into goals and we are not doing that and we had our more senior players who were unable to do it, we only scored from a penalty kick.
Sydney's 32nd-minute penalty for Del Piero was the subject of controversy as the foul appeared to take place outside the box.
Merrick felt the penalty was lucky to have been awarded but was also surprised when Wellington got their own second-half spot kicl.
"I didn't see either of them as been penalties actually, but I wasn't close enough to tell and I would never question our referees," he said.
Merrick noted the wet conditions were not any excuse for the result.
"I thought it was perfect weather, Scottish weather, that suited us," smiled Merrick.
"It's too easy to look for excuses like the weather etc, we competed well in the first half, two decisions went against us, two goals were scored and that was really the only time Del Piero caused any problems, but he took the penalty kick well and struck the free kick well.
"We spoke about it before the game not to give free kicks, but we kept giving away free kicks around the box and he punished us.
Merrick joked when he spoke about Wellington's good first half chances including the 35th-minute run from Jeremy Brockie which almost resulted in a goal but instead, after a brief fracas between the two sides, saw three players booked.
Merrick said: "Usually we get one of our players sent off as well.
"All I know is that next year we are going to have so much luck that it's going to be a different situation.
The former Melbourne Victory mentor wouldn't be drawn further on the goal-mouth incident in which it appeared Sydney's goalkeeper Vedran Janjetovic may have struck a Wellington player.
Janjetovic was eventually booked two minutes after the incident when referee Kris Griffiths-Jones spoke to the fourth official.
"There is no review of games any more so it doesn't matter now does it really, and the better team won.
"In the second half they did really well Sydney."
Wellington will close their season when they host Melbourne Victory at Westpac Stadium on Saturday.
