Thank you, but nope, I made the fill raster at the beginning of the project. I am doing this for a Udemy course on wetland delineation and such courses always start with filling the sinks. But I'll do the workflow again and see if I have better luck, unless there is another solution.
I was thinking it might have something to do with the outlet point, but if that was the case I would think the stream order tool wouldn't do anything with those incorrectly ordered streams.