Is there a way to prevent my follower becoming hostile towards Shadowmere?? They are driving me nuts, but I have a follower that once she's dismissed ou can never get her back, so I don't want to lose her quite yet.

Are different followers more or less likely to become hostile towards your allies?

On a side note, how do you get your follower to use the Azura soul gem??

Are you talking about Illia? Yeah she's annoying, a lot of times she'll hit Shadowmere with some ice spikes and then the two go at it. There really is no fix except to load a previous save, because if you try and clam her or use voice of the emperor like I did, she just walks away and won't be a follower anymore.

Ilia, my dark brotherhood initiate and brenlyn ( I think that's her name) have all been hostile with Shadowmere

I think the brotherhood initiate has been the worst with Shadowmere though, but I was thinking its because I gave her staffs, and she was hitting Shadowmere maybe because she isn't Mage trained?

What can happen is that Shadowmere is loyal to one person -- YOU. She loves you. She will come back from the dead to be with you. Your companions don't have VATS. If an enemy gets near you Shadowmere goes hostile, and your companion goes hostile toward it. But that misplaced swing or misplaced spell or fireball or splash damage from a staff hits Shadowmere from your companion, and your companion is essentially toast because unless your companion is about lvl 50 they're toast. I've seen Shadowmere take down two town guards, and I've seen three town guards take down a dragon. Think about that.

Side note: You have to equip your companion with a soul gem (I wouldn't waste Azura's Star on them because they'll kill a wolf), and you'll need to equip them with a soul trap weapon.