When do standard budget templates fall short for soft costs?

Hey everyone, I'm currently line producing a moderately-sized indie feature and finding myself consistently running over budget for what I'm calling 'soft costs.' I've been using a pretty standard industry budget template (the one that breaks everything down into typical above-the-line, below-the-line, post, etc.) but it feels like it just doesn't adequately capture things like comprehensive E&O insurance, all the little legal fees that pop up throughout development and production, or the often-overlooked demands of audit prep when dealing with investors. Every project seems to have these expenses ballooning. I try to pad categories, but it feels like guess-work. Has anyone found a more practical way to bake these recurring, often 'hidden,' soft costs into a budget from the get-go, before they become a nasty surprise? What budgeting approaches have worked for you when standard templates just don't cut it?