The draw meant Wales wasted a chance to seize control of Group B1.
The Czech Republic, their rivals for top spot, also dropped points in surprising fashion as they were held to a 1-1 home draw by Albania in a game which kicked off half an hour before Wales’ fixture in Podgorica.
Had Wales won, they would have needed only a draw in Tuesday’s final group game against the Czechs in Cardiff to secure first place, and therefore a more favourable play-off draw in the play-offs later this year.
Instead, Wilkinson’s side must beat the Czechs – who they drew with in the opening game of the campaign – to come out on top.
“We are exactly where we started [the day],” she added.
“We have to grab these opportunities. I’m sure the Czech Republic coach is as frustrated as I am.
“I am confident it will be a close game on Tuesday. We have to show up.”
The story of the night might have been different had goalline technology been in place at Montenegro’s Gradski Stadion.
Wales appeared convinced Hughes’ second-half effort had gone over the line before Montenegro defender Sladjana Bulatovic hooked the ball clear.
“I am frustrated there is no VAR, but this is the game – we can’t affect that,” Wilkinson said.
“I’ll fight for it behind the scenes, but on the night we needed to put the ball away.”
