Most likely at then it was done on purpose, sorta like those pranks you see in teen high school films/series where the geeky guy gets called out to some location only to get stood up or something just an embarrassing happen (ie. sprinklers going off).
In the flashback at the start of the film we see a young Killian who's rambles, stumbles and looks like your movie typical geek.
in the elevator we see this showing how Tony was dismissive to Killian
Aldrich Killian: Oh, now, that is an appropriate question. The ground floor, actually. I've got a proposal I'm putting together with myself. It's a privately funded think tank called, Advanced Idea Mechanics.
[he holds out two business cards towards Tony and Maya]
Maya Hansen: Okay.
[Maya takes the cards]
Tony Stark: Uh...she'll take both. One to throw away and one to not call.
following that after everyone gets off the elevator
Tony Stark: I'm titillated by the notion of working with you.
Aldrich Killian: Yeah?
Tony Stark: Yeah, cheese clown. I'm going to ditch these clowns; I'll see you up on the roof in five minutes.
[Tony steps out of the elevator]
Tony Stark: I'm just going to try to get my beef wet real quick. You know what I'm talkin' about?
Aldrich Killian: Okay. I'll see you up there.
Now we know that Tony is a different man than he was at the start of the series so it's odd that the "playboy" Tony back then would ditch the lovely group of ladies for Killian. especially if we assume that to "get [his] beef wet real quick" is to mean sex.
Also Tony's opening line into the flashback
We create our own demons. Who said that? What does that even mean? Doesn't matter, I said it cause he said it. So now he was famous and that's basically get said by two well known guys. I don't, uh...I'm gonna start again. Let's track this from the beginning.
and later in the film we return to the new years eve party where Killian contemplates suicide but then gets inspirations from the fact that no one would miss him, implying this was how he came up with the idea for the Mandarin.
considering the damage Killian does to Tony and almost loosing Pepper a few times because of him we can assume the "demons" Tony is referring to here is Killian and how, because of his mistreatment of him, created the Mandarin. backed up with Tony's monologue at the end of the flashback
So why am I telling you this? Because I had just created demons, and I didn't even know it.
Now aside from just being a jerk back then and wanting to ditch the "nerd" another possible motivation for Tony to trick Killian like that could be because Killian was giving attention to someone else
Aldrich Killian: Mr. Stark! Oh, wow! Hey, Tony! Aldrich Killian. [to Maya] I'm a big fan of your work!
Maya Hansen: My work?
Tony Stark: Who isn't? She needs me.
Aldrich Killian: Well, of course. But, Miss Hansen, my organization has been tracking your research since year two of MIT.
and we see that in the elevator Killian was giving Maya the card and asking her to join AIM instead of Tony so Tony probably felt that he was being disrespected by Killian and wanted to get back at him
now given the kind of "prank" this is Tony probably did end up forgetting he sent Killian up to the roof at the time when he became intrigued by Extremis and later hooked up with Maya, though on a whole Tony says at the end of the flashback that he forgot about that night
Yeah, those were the good times. Then I moved on. After a brief soiree in an Afghan cave, I said goodbye to the party scene. Forgot that night in Switzerland. These days I'm a changed man, I'm different now. I'm well... you know who I am.
Script Source: Transcripts Wikia > Iron Man 3