You must make sure that you - not AC - decide the tread sizes etc. What might be the issue is that you have a fraction of a step at the top of that angled intersection. Look at stairs I made from exact same fill/travel lines.
On the left AC made all geometry choices. On right I figured out what would create perfect tread geometries, and by unlocking the AC default values you can change the run/rise, tread etc. View is from underneath.
When you MUST have a partial tread at the landing, then create each run separately and drag them up to the correct elevation. Piece the stair together from separate parts.
