Examples of astrophysical objects NOT in virial equilibrium?
Not clear what the initial part of your question means. Objects can be in virial equilibrium without being in thermal equilibrium.

A clear exception to the virial theorem would be any system that is gravitationally unbound. So you couldn't apply it to a supernova explosion or a dissolving cluster of stars.

The examples you quote are not self-gravitating, bound systems, so no, the virial theorem would not apply to them.