The Primeira Liga side appeared to be in control for much of the match on Wednesday and saw a host of opportunities go begging - with Andre Carrillo firing straight at goalkeeper Jasmin Handanovic in the 26th minute before collecting the rebound and striking the crossbar.
Nevertheless, Nani appeared to have given them a crucial win with a low strike in the 80th minute to open the scoring.
But Maribor clinched a dramatic late equaliser in stoppage time, as substitute Luka Zahovic came off the bench to rescue a Group G point.
The Portugal-born son of former Benfica attacking midfielder Zlatko Zahovic capitalised on Mauricio's sliced clearance to nod in the equaliser, leaving Silva unimpressed by his team's inability to see the match out.
"We should have got the win," he said. "Also, we missed goal chances. We could have killed the game at 1-0.
"We will learn, but it is not a good thing that this happens. We know that there are times that we create two or three chances and score them, and then there are moments like this.
"Most worrying are the defensive moments which we need to rectify. This worries me most, honestly. There are defensive aspects we need to improve.
"We proved that we were superior. We added a point away from home.
"A win here would have been a good, strong start, but we cannot let it demoralise us because we have a very important game on Sunday [against Gil Vicente in the league]."
