I tried looking this up but haven't found much. I'm a Nord Stormcloak by the way. I was on a journey with Faendal traveling to my next objective and I spotted some Imperial guards. I decided to ambush them. I took out one of them and then looked behind me to see what Faendal was up to. I assumed that Faendal would back me up but instead he became hostile towards me. I finished off the other guards and had no choice but to put Faendal down. I'm curious as to why he would attack me just for attacking some soldiers. He's from Whiterun Hold and supposedly has no affiliation with the Empire so why would he turn on me?

because if you look up faendal his morality is "no crime" meaning if you do an unjust act just as attack a guard who was not attacking you for example he will join your enemies and try to kill you. It seems they changed this in the legendary addition as when I tried that he doesn't turn on me.

Along similar lines, I find that if you have multiple Followers, they can end up attacking each other. In vanilla you can have just one Follower + one dog. With Dawnguard, I believe you are allowed to add Serena. I use Serena as an armored mage, so she's using staffs and spells and often slinging around area of effect spells like Fireball. If she singes one of the other Followers, they will often end up attacking her in retaliation. That forces me to Load the last Save and hope she doesn't do the same thing next time around.

Spellcaster followers can be a real bind especially if you're in a town when a dragon or vampires attack.

A similar thing happened with me and him. After taking care of some vampires in Whiterun I accidentally struck a guard. He retalliated against me. I escaped and returned to Riverwood about a week later where he was the only one hostile towards me. I ended him there.

Faendal seems to have a lawful "disposition" so attacking guards and Imperial Soldiers will cause him to turn on you. Also, you can't order him to attack hold guards and innocent citizens.