I heard the Shimano Saint has some compatability issues. Is it with a bottom bracket? or crankarms
or other non-Shimano Saint chainrings?

Since Shimano traditionally used a standard 2-degree square BB spindle taper with an oddball end dimension, and since chainring BCDs and BB shells are pretty well standardized, I would not be at all surprised if there were some sort of problem in crank-to-spindle fit.

Saint uses the new shimano bb with outbound bearings and 2 piece cranks (Hollowtech II?). Since you can only use a shimano bb I doubt it has problems.
I guess the problems if they exist could be with rings, frames or guides.