In the described case, this was a simple user error. But you are right nonetheless: To enable the concurrency, the system uses a parallel inference kernel (https://www21.in.tum.de/~wenzelm/papers/parallel-isabelle.pd...). I have heard the anecdote that in the first version, this also allowed one to prove false, by fulfilling a proof promise with a proof that depended recursively on the same promise.

And there are verification tools for verification tools! Isabelle has a verified proof checker that can check whether a given proof is sound: https://www21.in.tum.de/~rosskops/papers/metalogic_pre.pdf The only caveat is that the proof checker itself is verified in Isabelle...