I know the frustration. I’ve seen planar elements get corrupted, and it’s hard to know just when and why it happened. I often us “Save As…” to leave versions of my model as I go, and can go back and retrieve parts from if need be (i.e. find a previous version before the corruption crept in). As john_drivenupthewall says, Show Hidden Geometry helps debug the mess. Here’s an example I had a little while ago.
This aught to be a simple flat face with one door cut in, but hidden geometry is even connected to other faces not touching it. Copying just that face from a previous version wasn’t good enough. I had to explode and recreate a new group.