Gnuplot has several limitations including complex functions not working for gamma and Bessel functions, commands after a load filename being ignored, error bars not being properly handled in polar/spherical plots, and floating point exceptions occasionally being generated by user defined functions. It also has issues with the nohidden3d option not working for parametric curves, time coordinates wrapping at 24 hours with 1 second precision limiting geographic plots, and only one color palette being active per x11 window.