While completing the Knights of the Nine quest I received Lord Vlindrel's curse from the cursed sword when I equipped it to cleanse it at the alter in Cheydinhal. Anyway after completing the rest of the quests for the Knights of the Nine I continued to go back to the Main Quest (Taking civilians out of the Church in Kvatch and Saving Castle Kavtch.) I have made it a point in my game to be a "hero" per say so I haven't been stealing any items and for some reason I think because of this curse I keep getting bounty's on my head for over 1,000 gold in Cheydinhal and I haven't stolen anything? Help removing the curse would be very appreciated.

Lord Vlindrel's curse has no other effects than the elemental weaknesses it applies, and it should be removed by the end of the Knights of the Nine questline.

Bounties of 1000 gold mean that you've been murdering people; either deliberately, or by accident in combat with NPCs helping you. Have you?

To be clear: it isn't murder if the NPC attacks you first, unless they're a guardsman. You'll know if you've committed a murder if a message appears in the corner of the screen saying that your screen saying that the killing has been observed; also check the statistics page to see exactly how many murders you've done total, if any.

Other than murder and stealing, the only way to get a bounty that high is being caught repeatedly for pickpocketing, assault, or trespass (but understand that you've have to commit hundreds of trespasses and nearly fifty assaults or pickpocketing to get it that high), or by accusing one guardsman of corruption during a quest.

I did accidentally kill one of my knights during a quest a message popped up in the corner saying that the gods will watch how many times that happens and take away the crusaders weapons if they notice again. I checked my stats and I have 3 assaults and 1 murder is this why?

Yes; it is annoying, but sometimes NPC allies get in the way and you accidentally hit them. Normally they warn you if you do, but if they have low health, they may doe and you get blamed for it.

Nothing else to do but pay the fine. You can still wear the Crusader's armor, but if you get another point of infamy, you won't be able to. You can reset your infamy if you do the Pilgrimage again, though.

But don't worry about assaults; the game counts it as an assault if you, say, sneak attack a bandit or something else that would usually attack you first.