For anyone down at the bottom there is a sense of inevitability that the breaks will go to the opposition. This was Stoke City’s lament. They had held their own at a typically edgy Emirates Stadium until Bruno Martins Indi stretched into a penalty-box challenge on Mesut Özil in the 74th minute.

It looked clumsy and a little risky but TV replays confirmed that Martins Indi had got a toe to the ball. Craig Pawson’s penalty award felt like a kick to the guts.

Stoke have only ever tasted defeat at this venue – their last away win againstArsenal came at Highbury in 1981 – and Pierre-Emerick Aubameyang set the latest reverse in motion when he converted the penalty.

Arsenal were dreadful in the first half and it was easy to think they had their minds on the Europa League quarter-final first leg against CSKA Moscow on Thursday night. But the roof fell in on Stoke after the first penalty and Paul Lambert could not hide the frustration.Aubameyang added a lovely second before the substitute Alexandre Lacazette gave the scoreline a gloss that had not looked likely at half-time – when Arsenal were booed off – with another penalty. It was Lacazette’s first action since mid-February and knee surgery. He had replaced Danny Welbeck, who suffered a back problem.

“I respect the referees,” the Stoke manager said. “I just think in big moments in big games, you have to be 100% sure. It was a game-changer. It was pretty soft.”

Martins Indi said: “I touched the ball and it was not a penalty. The referee’s angle was not good enough. He said that I stretched my leg and made a foul. He needs to watch it again. The cameras don’t lie.”

Lambert made the point that moments earlier Xherdan Shaqiri had curled an inswinging corner against the far post. Not for the first time during his nine-match tenure, he and his team were on the wrong side of the finest of margins.

It should be said that Stoke’s lack of goals remains a huge concern – they have scored only four in eight matches. But there were pleasing aspects to the performance, particularly in the first half, in terms of their discipline and the platform they constructed to press into the final third.

“I am still 100% confident we will stay up,” Lambert said. “The only thing missing from our game is Lady Luck.”

Arsenal’s preoccupation with the Europa League was reflected in Wenger’s lineup – he rested a clutch of players – and by that in the stands. There had been a virtual full house for the second leg of the Milan tie in the last 16 of Europe’s second-tier competition but there were thousands of empty seats here. It had been the same story for the previous home league fixtures against Watford and Manchester City. Wenger blamed the “family happening” of Easter Sunday but he did concede that the turn-out was influenced by the fact his team “don’t go for a lot in the league”.

Lambert went through agonies in the first half as Stoke worked a few promising breaks only to miss the final pass or dribble. Shaqiri bent a shot just wide on four minutes while Joe Allen caught the eye with his skills in tight areas, passing and pressing.

Aaron Ramsey managed a deft chip up and against the crossbar in the 24th minute but, that apart, it was lethargic stuff from Arsenal before the interval. Their game was marked by sloppiness and a lack of structure in attacking areas. Wenger said he felt “we could lose in the first half”.

Mohamed Elneny saw a shot blocked by Martins Indi in the 59th minute and Arsenal turned the screw with 20 minutes to go. Jack Butland denied Aubameyang one-on-one after Özil’s through-ball; Calum Chambers could not finish from a corner and it took the first penalty award to break Stoke. It was worrying to see how they folded thereafter. Ramsey rounded Butland but could not convert; the goalkeeper blocked from the substitute Henrikh Mkhitaryan and he also punched clear from Özil. From the corner, when the ball broke to Aubameyang, he cut across his shot to send it screaming past Butland.

The second penalty followed Badou Ndiaye’s barge on Lacazette. It was robust, needless and, as Lambert admitted, it gave the officials a decision to make. Aubameyang, who had the name of his late grandmother, Marina, cut into his hairstyle, eschewed a potential hat-trick by allowing Lacazette to step forward.

“It shows well the state of our society that, when people are generous, we are surprised,” Wenger said. “We are even more surprised when it is footballers and strikers.”