Wells’ side came into the game unbeaten in the West Yorkshire Premier Division whilst Boroughbridge had endured five straight defeats in their opening fixtures.
However, Mike Mullenger’s 83rd minute strike handed Boroughbridge the points and Wells praised his opponent’s approach to the game.
He said: “The Boroughbridge lads just wanted the win more. They knew it was a matter of who wanted it most.
“It was a local derby so there were bragging rights at stake. Before we started the warm up I told the lads they have to be on top of their game otherwise they would be found out.
“We did not put in the performance we should have done but Boroughbridge did the right thing. They were well drilled, well organised and played some nice football.
“Our lads have played very well this season and we have been riding the crest of a wave but this is a great leveller.”
Wells admitted he was disappointed with the result and reiterated that his players needed to think more ‘intelligently’ about their game.
He said: “We can all play football, do nice tricks and work as a unit but we need to read a game better and that will challenge us.”
The Reserves now face a tough run of fixtures in the Premier Division including a home game against Leeds City and league leaders Field on Saturday.
Wells said: “Field are as good as the position they are in the league. They are a big strong team and we have to match that.
“We have to be on top of our game. We have a lot of kids from our academy playing for us so this is possibly their biggest challenge but I’m hoping they will rise to it.”