Bon Bon is in Canterlot often enough, hanging around in high society circles.
 
As for the wedding, why are only Lyra, Twinkleshine and Minuette the bridesmaids? Where is everypony else?  
– Bon Bon is mingling with the elite while secretly monitoring the scene. Since she is dressed up to the nines, she’s somewhat hard to identify. She was both invited by Fancy Pants and assigned by Celestia before Lyra could have invited her. Not unlikely that it was actually Celestia who paid for Bon Bon’s fancy outfit. In fact, Bon Bon is around when her boss is shot down by Chrysalis. I guess she’s glad that the Mane Six take things into their own hooves. I’m not sure whether the Agency was prepared for changelings, but Agent Sweetie Drops doesn’t do anything.  
– Lemon Hearts organises the whole shebang. We know now that that’s her job. When her friends come back from the cave in time for playing the fanfare (at which point Lemon Hearts leaves the rest of the ceremony to Celestia), they either don’t remember what happened in the cave due to Chrysalis’ magic, or the do remember, they tell Lemon Hearts, but she decides to leave the changeling problem to professionals (although one of their leaders is out of duty because he’s getting married).  
– Twilight and her new friends are already scheduled to be additional bridesmaids, seeing as Twilight is not only the groom’s sister, but she used to be babysat by the bride. However, Twilight mysteriously vanishes before the ceremony. Lyra & Co. probably soon find out why when Chrysalis sends them into the cave.  
– Moondancer would probably never attend such an event, especially not if Twilight’s presence is to be expected. Maybe Lyra tries to get her to help when the Changelings attack, because for all we know, Lyra is outside during the invasion.

Hmm, I get it now!  
Twilight Sparkle lived in Canterlot as a filly, but when grew older since Season 1, she lived in Ponyville.

Because they must be seen spending every minute of their lives together. O_o

@marinus18
 

 
See 621Chopsuey’s comment

Lyra didn’t meet Bonbon until after she moved to ponyville.

bon bon took the picture.

“Hey BonBon Twilight invited me to catch we our freinds in Canterlot want to come?”  
“Um sorry Lyra but um I got secret agent stuff to do see ya.”  
“You always say that when I try to introduce to my old friends.”

@Background Pony #D000  
Actually, they might have at least met at that one party in Cheese’s flashback.
 

@Marvelous TK
 
Also the bottom picture is from before Twilight moved to Ponyville, we don’t even know if she was friends with Bon Bon yet.

@Marvelous TK  
A wedding that was on high alert due to security threats. I’m thinking the Agency was a bit busy that day.

@Mildgyth  
So the top picture is specifically of Lyra as a bridesmaid, with her fellow bridesmaids, helping prepare for a wedding?
 
And OP thinks Bonbon should have been dropped into that setting because…?

@Apple Senior
 
The top picture is from A Canterlot Wedding. Twilight was already in Ponyville.

How can you know? Both pictures are from the time when Twilight was still in Canterlot. When Lyra moved to Ponyville after Twilight, she maybe didn’t even know BonBon at the time of the Pictures.

@WM-R  
Sure, I agree with that.
 
And that.

Agent Sweetie Drops was on the mission and could not take the invitation.

@Ilsor
 
This is true, but you don’t normally do that with a, “Hey, it’s been years! Wanna get together with the old gang sometime?” type situation, do you?
 
I mean, I always figured you’d normally go, “Hey, mind if I bring someone with me next time?” If I haven’t seen a friend in ages and I ask them out, I’d actually like to spend time with my old friend, at least at first.

Are they not allowed to have lives that don’t ALWAYS involve the other, or must we stitch them together for all eternity and they cannot ever be apart?

@WM-R  
Sometimes I do, if I feel that they can befriend each other.

Wouldn’t it be more likely that Bon Bon was busy and she couldn’t go?
 
And plus, she might have been there at A Canterlot Wedding.
 

@Roy-of-Asturia
 
Plus, do you normally invite your best friends/roommates/significant others to join you when you go out with old friends? Seems kind of inconsiderate.

We should stop shoving rubbish down our gullets.
 
Bon2 / SD has her own untold story.