- GR breaks down when you go to quantum levels
Could you be more specific? There are plenty of successful marriages of GR and QM. For example quantum field theories such as QED, QCD etc.
- GR does not fully describe black holes (particularly their horizon and the singularity)
No one has seen the event horizon or the inside of a black hole so we don't know if the GR predictions matches reality or not. (And, if GR is correct, nothing beyond the horizon can be studied). The things we have checked (like gravitational waves) matches.
- GR is incomplete with regards to explaining the expansion of the universe (the discrepancy is called Dark Energy)
Dark Energy is a proposed solution to make the observations match the predictions. So, if dark energy is found there is no conflict with GR. Calling GR incomplete is a bit unfair since it isn't a theory of everything (and isn't supposed to be), just a theory of the interaction between matter/energy and spacetime. It makes no predictions of how much or which type of matter should exist.
I'd say the original statement holds. No cracks have been found yet.