E.g., Metamath is designed to be as theoretically simple as possible, to the point that it's widely considered a toy in comparison to 'serious' proof systems: a verifier is mainly just responsible for pushing around symbols and strings. In spite of this simplicity, I was able to find soundness bugs in a couple major verifiers, simply because few people use the project to begin with, and even fewer take the time to pore over the implementations.
So I'd be hesitant to start saying that one approach is inherently more or less bug-prone than another, except to be slightly warier in general of larger or less accessible kernels.
The linked blog post says "Unfortunately, a student once submitted work containing this error; it was almost entirely incorrect and he had no idea." I guess the student probably was aware that not every proof had gone through, and that the that he saw like "99 out of 100 proofs succeeded" and assumed that meant that he had mostly completed the task, not realizing that a false theorem would be used to the give incorrect proofs for the rest of the file.
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...