Let’s focus on the problem rather than finding fault. I agree with the assessment to wait and monitor. Yes, there’s a chance that apicoectomy is needed if the lesion expands or if symptoms develop down the line. But retreatment was still the best first step. Now the question is if apicoectomy is also needed at some point or not. You should restore the tooth right away with a definitive filling. You can wait for the crown if needed; but do not wait with a provisional for an extended period “to see what happens” as it can get cause a separate problem. It’s not as bad as situation as you may think. The overextension of the material/file is not necessarily a problem; and if a problem comes up (pain/swelling) apicoectomy by an experienced surgeon/endodontist will have a good prognosis. Good luck.