How do I prevent overexposed windows from bleeding into the other exposures in a 3-shot bracket?

Include a dark enough bottom-level exposure. The rule of thumb: AutoHDR can create a window view only as good as the window view in your darkest bracket.

Why this happens

If your darkest bracket still has blown-out windows, there's no clean data for the AI to pull from. The brightness bleeds into the blend.

The fix

When shooting, check that your lowest exposure is dark enough to clearly see outside the windows — windows should not be blown out in that frame. The model can only create an edit from the data your brackets actually contain.