I don't know what the OP was referring to specifically, but the rivers in FT have some problems (at least they had in FT2, I haven't tried FT3) in that they don't precisely follow the terrain configuration, but only roughly so. Sometimes they appear to flow upward (going over small hills etc), and often they end a few pixels before meeting the sea. Sometimes they go in circle, especially when two or more meet.
Moreover, even when they don't have glaring errors, at close zoom levels they are always too straight ant not enough "serpentine".
Overall, the rivers produced by FT may be used as a guide, but you would be better off painting over them and correct any error that there may be. They may work well on their own only in the very lowest levels of zoom (like, worldwide map).