You're probably best keeping them separate for now, till she's spayed. Buns remember things, and you don't want to mess up your chances of bonding them later on if there is any issues now. Remember that. You do want to see them happy together, but you'll have to wait a while if you want that to happen.
Good luck!

One thing that I am concerned about -- how long ago was he neutered? He needs to be separated for at least a month or two from her (if she is unspayed) because he can still impregnate her if his hormones are still there.

The main thing with bonding is to ENSURE that all play dates end on a good note. The only way buns can bond is by figuring out what the hierarchy is between the buns you are bonding. They NEED to work this out to effectively bond. Having Play Dates before the surgery isn't necessarily a bad thing but you have to work to ensure that each bond session ends on a GOOD note. Whether it's simply you giving them treats with one on either side of you or they make a friendly little gesture towards each other. If they have been charging each other -- maybe if one day they simply don't charge each other... and sniff around each other -- you can give them a few minutes and then put them away and do another bond session tomorrow. Most people choose to wait until after the surgery before attempting play dates and bonding but as someone who did most of the work before my trios surgery, it's definitely not impossible if done in the right way.

The great thing about young buns -- is they seem to be very accepting of other bunnies. Once they decide who the "top bun" is! One question, what exactly do you mean by charging? Do they run directly at each other and circle each other? Or do they charge and nip and bite? If they are not nipping and biting at each other that is a VERY good sign.

I think it sounds very promising for a good eventual bond. I would schedule her appointment as soon as possible, just to get it done so you can proceed. I think one month after his neuter should be enough to be safe around her (no less) but just before that he may have a final surge of hormones so you do need to be careful. But it sounds as though, if there is no biting involved, that supervised sessions are going to work even now, for short visits, as they get used to each other's presence and smells.

He was neutered over 2 months ago so there is no chance of accidental babies.

He runs at her and then stops when he is close to her. No circling yet. He nips her a little but no bites (thankfully). The nips are when they are sitting next to each other and she is still but he doesn't nip her after running at her. When he charges her he just gets to her and lowers his head. I am assuming this is so that she can lick it but she doesn't make any move. He normally charges her after she moves so I am assuming that this is because he gets a fright.

Bambam knows other animals and his best friend is my moms cat. They follow each other everywhere!! So not sure why it is so different with Pebbles

It sounds like to me they are just trying to establish their bunny "hierarchy" and haven't come to terms with who the top bun is going to be! LOL. I wouldn't worry -- this is all normal behavior during bonding! It seems like he is DEMANDING some grooming and your little girl is saying "no lovin' for you, tough guy!" It sounds like you aren't going to have much trouble with bonding, especially after she is spayed. My girl was a lot more willing to groom and accept the boys after her spay but there were no flat-out fights before that. She ignored them both for awhile until SHE decided she was interested -- then it just slowly started a bond from there! Seems to be a girl thing! The boys were ALWAYS trying to love on her though, LOL. So I wouldn't be worried or frustrated at all yet -- sounds like everything is going smoothly! Slowly but smoothly! Which is much better than most people get in the beginning.

Thanks so much for all your help. They are getting a bit better and I have been doing 10-20 minute bonding sessions a day. What confuses me is when she is in the cage they will both be flopped next to each other but when Pebbles comes out for play time Bambam nips her and growls. I try to give him as much attention as I can and let Pebbles run freely in my room but he still runs at her. I dont know what else to do!