Alan Pardew's side saw two Papiss Cisse goals ruled out by the officials despite replays suggesting that there was no infringement in either strike.
Krul told the club's official website: "We should have won this game, definitely. We created so many chances but it's a shame we didn't finish them.
"I would have liked to have put it in the back of the net myself but I can't! But we have to take the positives as well."
The second leg of the tie takes place next week when Newcastle travel to the Ukraine, looking to book their place in the last 16 of the competition.