Incompatibility of programs between different distributions.

Some configurations could be very complicated for a common user.

Incompatibility with some graphics cards and devices.

Finally and most importantly, some applications such as games, image and video editing programs, among others are not available for Linux, for example, Adobe Suite, 3D Studio Max, Visual Studio,etc. There are alternatives but they don't even come close. This is not a defect of the operating system but of a commercial alliance.