Shy guys, why do they tend to ignore the girl they like?

I think one reason might be the expectations he has.
See, he probably feels he's supposed to be doing something, but he doesn't know what exactly. And now that you've started flirting back with him, the stakes have been raised. Before, he could have just pretended that there's no way you'd even notice him. Now he's not so sure.
Assuming you're reading the signals right, and I think you are, he's definitely interested in you.
That hasn't changed. It's not like one day he's into you, the next he's not. Guys don't work like that. What's happening when he seems to ignore you and retreats, is that he feels like he's playing a chess game and he's in a stalemate situation. So he's nervous.
So he retreats to plan his next move. It's the natural behavior of a shy guy. During that downtime when he doesn't know what to do, he tries to not do anything, which could come off as ignoring you.
How long this could go on depends on the guy. Some shy guys will trap themselves in a stalemate indefinitely, never getting out of it, even though the trap is mostly created by the own mind. The key, I think, to overcoming this is you have to convince the guy to let go of his expectations, because as long as he feels everything is so important that he has to second-guess everything he does, he won't get anywhere. Easier said that done.
It's a tough situation because you're shy too, although I don't know if guy shyness and girl shyness are always for the same reasons. But regardless, someone has to break the ice.
The ignoring thing might just be that he's distracted by a busy schedule. I have to really focus when I need to sometimes and everything fades to the background but my task at hand (even the women I would like to start relationships with). That he shifts phases makes me almost certain he's just bogged down by his work/class/schedule and he is still very interested in you.
Sometimes I also feel like I stare too much at women and shy away when I cannot read them. I mean, there's a girl I kind of like but I cannot tell if she is smiling to be nice or if she is smiling because she is interested in getting to know me better. I would hate to have her break it to me that she is just smiling to be nice and really thinks I'm creepy for approaching/staring at her all of the time. I don't want to be a creep! So I had better not stare too much or I am automatically on her blacklist =( SMILING DOESN'T TELL ME SHE IS FLIRTING WITH ME. IT TELLS ME SHE IS A NICE PERSON IN GENERAL AND PROBABLY SMILES AT A LOT OF PEOPLE.
Do this: ask him if he'd like to get food with you. Maybe bring friends, too, if it seems awkward the first time. Ultimately you want to go out with him alone at some point and ask him how he feels about you.
Aw try walking up to him and giving him a little assurance.
It's good that you're comfortable staring at him. Now he's feeling the moment getting bigger and bigger and he's starting to doubt himself. He must like to flirt but when it comes to taking the next stop he's shy just like everyone else.
Im in this exact situation and its so frustrating getting those mixed signals specially because I left my ex boyfriend because i couldn't get him out of my head!
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U gotta be the "man" and ask him out in this situation I think:P that guy is to SHY and may have veyr low selfconfident. Best way is that you take the first step and see how it goes:)^^ Good luck:D
Ask him out or something. Seems he likes you, but is unable to tell if you like him.
Because I don't want to be rejected.
cuz they're shy, duh.
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