The Spaniard insisted that Daniel MacKay was offside when he nodded home the Easter Road side's second goal from close range after Paul Hanlon headed a Kyle Magennis corner back across goal.
The goal, MacKay's second of pre-season after also finding the net against Dunfermline, sealed an impressive 2-1 friendly victory over the Engish Premier League side, who were playing their first warm-up match following the summer break.
Arteta said: "I'm always disappointed when we lose a football match but it is the first game, we played with many kids and we only had four training sessions.
"We've trained really hard and you could see that the players were a little bit leggy. I think we conceded the first goal, an accident, and the second goal was clearly offside. We created many, many chances but we didn't score. That's what pre-season is for, to take the things that we haven't done well into a training session and then improve."
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Hibs had taken a first half lead through Martin Boyle after the Australian front man capitalised on an error from 19-year-old Gunners goalkeeper Arthur Okonkwo.
MacKay's goal followed midway through the second half, then Kevin Dabrowksi saved a penalty from Arsenal forward Nicolas Pepe before Emile Smith Rowe pulled one back for the Londoners late on.
Even accounting for the fact Arsenal did not have their full line-up and were playing their first pre-season fixture, it was nonetheless an encouraging result for Jack Ross’ men against a side boasting multi-million pound talent, such as £72m man Pepe and £56m striker Pierre-Emerick Aubameyang.
Arteta felt his team's lack of training thus far was a factor in the defeat.
"It does but there's no excuse because we want to come here and win the match," he told the Arsenal website.
"They worked really hard, the boys worked really hard and you could see that some of them were not in the best condition, but we're still very early in pre-season. It was great to see some of the young lads making their debuts here. We'll keep working."