He is jealous.
Eren does not quite know why he is jealous, but he is absolutely feeling jealousy. He sees the way Jean looks at Mikasa and he does inot/i like it. Ever since their days in training, Eren has seen the way Jean looks at her. He never has liked it. (He at least got some revenge when he overhead Jean saying he liked Mikasa's long hair and he convinced her to cut it so it would not get stuck in their 3D maneuver gear. Part of it was a legitimate concern, but most of it was fueled by the need to spite Jean.)
There are times when he sees Jean try to make a move; he fails, of course. Jean is a horrible romantic. He gets too flustered over pretty girls and Eren is at least glad Jean can never get too far with his advances. But still, he watches as Jean continuously tries his hand with Mikasa, and Eren cannot stand it.
One day, he gets his chance to bring up the topic with the other boy. Eren has not prepared what to say. He lets his emotions take over just as he always does. He still cannot pinpoint what it is that he is jealous about. He just knows that he does not like the idea of Jean fawning over Mikasa and he will not stand by to let it happen.
"Stay away from her."
"Huh?"
Eren seethes. Jean should know exactly what Eren is talking about, yet, it appears he does not. Or, he is playing dumb. Eren cannot tell.
"Stay away from Mikasa."
A smirk spreads across his face and he asks, "That's what this is about?"
The remark makes him angry. Jean should know better; he should know that Mikasa is off-limits. Eren questions himself, though: Why is Mikasa off-limits? Is it that he does not want Jean to be with his childhood friend? Or, is it something is?
There it is again: iWhy/i is Eren jealous? Why is it that he cannot stand to see Jean attempt to win over Mikasa? Is it that he feels a rivalry with Jean or is it that maybe Eren feels more for Mikasa than he realizes?
"She doesn't want anything to do with you. Leave her alone."
Who is Eren to speak for Mikasa, though? Who is he to say that she has no want to have a relationship with Jean? Is he simply letting his own wants get in the way? He has never discussed anything about romance with Mikasa, so who is he to say that she does not want to be with Jean? Is it that, perhaps, Eren simply wants her to himself?
Mikasa passes by—to where, Eren has no clue—and turns to see the two as things are about to get heated. "Eren? What are you doing?"
A smile spreads across Eren's face. He flashes it in Jean's direction. He can prove that Mikasa wants nothing to do with Jean. Eren once again lets his emotions get the best of him. He rushes over to Mikasa, grabbing her by the shoulders, smashing their mouths together. It takes her no time to return the kiss. She is surprised, but she does not question it. Both are happy with this outcome.