Emery was frustrated as his side came away from the Amex Stadium with a 1-1 draw.
Pierre-Emerick Aubameyang had given Arsenal a seventh-minute lead but Jurgen Locadia took advantage of a Stephan Lichtsteiner mistake to level just before half-time.
As the full-time whistle blew, Emery’s emotions spilled over and he booted the bottle in the crowd.
But he quickly went over the say sorry for his actions.
“I said to them apologies because I kick the bottle after a disappointing action for us in the last minutes,” Emery said.
“It wasn’t hard, but it touched one supporter for them.
“I said to them I’m sorry.”
Emery’s substitutes during the match were questionable as Mesut Ozil was taken off at half-time and striker Alexandre Lacazette was replaced by midfielder Aaron Ramsey shortly after the hour mark, despite chasing the game.
“I think Aaron Ramsey deserved to play,” Emery explained.
“He deserved to take the responsibility because he wants to help us.
“I think Aaron played a good match today in this moment.
“[Ozil] was only tactically. We did before, in other matches also change the idea from the first half with other players.
“And today I did it with Mesut, that is only tactically, not another problem.
“Tactically some matches I did that. I wanted to control better the positioning on the pitch, but in the second half we couldn’t do our ideas on the pitch to impose.
“We created less chances in the second half.”