Fired for cause

I was recently fired from my job for working from home without permission.

If I am open and honest about this on my forms, would this be a reason to be denied security clearance. This is the only thing that could possibly raise a red flag.

If that is the only reason for your termination and there has been no similar conduct or rules violations then it should not prevent you from being eligible for a clearance. However, if there were other reasons and they become known during the course of the investigation then it may be viewed as a lack of candor.