You can't do anything in those cases where the algorithm identifies the wrong overlap areas. Photoshop has the same problem. It often doesn't do this right but is usually a bit better as you have observed. In those cases only option is to use real panorama stitching software where you can identify to the software which regions match.
I've found that stitching by Photoshop to highly accurate. I do not recall an panorama that failed, even with "high frequency" details like tree branches and window lattices in sky scrapers. But, when I encounter an image Photoshop cannot handle, what software are you using? Thanks.
I get many situations where Photoshop gives crooked horizons unfixable by
the wide angle filter and where it misaligns even images shot on my nodal
ninja (where there is zero parallax). It gets confused easily. Not as
easily as Lightroom but still. The software I used most is hugin. An open
source set of utilities. Quite a steep learning curve but extraordinary
quality. I also shoot a lot of fully immersive panoramas. Neither Photoshop
nor Lightroom can stitch those correctly.
I've used the Transform-->Warp to straighten Photoshop panoramas. It's not always perfect. I'll have to try Hugin. Thanks for the tip.