Logos with photographic elements. If the logo contains a photo, the tool will cut out the photo, not the logo from the background of the photo. This is the same limitation as any segmentation tool.
Logos with gradients that extend into the background. If the gradient fades into the background colour, the cutout will produce a hard edge where the gradient used to continue. This is a design problem, not a tool problem.
Very low-resolution logos. If the source is small, the cutout is small. Use the highest resolution version you have. If you only have a small version, consider redrawing the logo as a vector rather than trying to salvage the small raster.