Wenger's men fell behind after just 19 seconds at the Britannia Stadium in the Premier League clash when Peter Crouch put the hosts ahead before Bojan Krkic and Jonathan Walters scored to seemingly put Stoke in complete control at half-time.
Stoke were aggrieved to see a potential fourth goal disallowed as Bojan's second was chalked off, Taylor adjudging Mame Biram Diouf to have interfered with play from an offside position.
That decision sparked an Arsenal fightback as a Santi Cazorla penalty and a fine volley from Aaron Ramsey got the visitors back into the game.
However, Calum Chambers was dismissed after receiving a second yellow card 12 minutes from time for pulling back Bojan to leave Arsenal with too much to do and Wenger fuming at Taylor.
The Frenchman took issue with Walters' strike, which he believed came after a foul in the build-up as Crouch knocked the ball down to the Republic of Ireland international, and stressed that Chambers did not deserve to be sent off.
"I feel we were a bit unlucky because the third goal was a foul on a corner," Wenger said. "Still, we were defensively not good enough.
"It [the red card] was a bad decision, if Chambers has to go out I can watch with you the game and I find you five more players who should go out.
"Watch the game again and I don't think that Chambers deserved to be sent off compared to some other people that put arms and elbows in faces."
Despite his anger at the refereeing decisions, Wenger identified his side's inability to deal with injuries at the back as the main reason for their defeat.
"Stoke started strong and we were not decisive enough in the defensive challenges," he added.
"We were too tender at the back from the start and when we started to respond it was late in the game.
"We were a bit inexperienced at the back, we could not play [Laurent] Koscielny, we could not play [Nacho] Monreal and with [Mathieu] Debuchy being out as well we were altogether a bit soft to cope with what they offered us."
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