The draw meant Wales wasted a chance to seize control of Group B1.
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 goal-line 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.”