Water ripples, waves, white “streaming” etc., that isn’t in the same place in each part of an overlapped frame - and therefore doesn’t stitch well - can hardly be blamed on the stitching software. Layer blending in PS for those parts of the image would be better to “patch” the bad areas.
In general, water notwithstanding, I’d say that making sure the pan head is dead level, and that camera/lens position has been adjusted to eliminate parallax, is important for any stitching software in order to get a truly seamless stitch.
I’ve had zero problems using LrC’s stitch feature.
This is seven vertical frames, stitched in LrC, 30mm lens (24mm FF equivalent), Arca C1 head, RRS Nodal Slide:
Rand