[Refactor] Address S101 violations in cyto_utils

[kenibrewer]

#387 introduced Bandit checks. Several S101 violations in pycytominer.cyto_utils were left unaddressed at that time and were instead given # noqa: S101 ignores.

Acceptance Criteria:

• There are no # noqa: S101 ignores in the pycytominer repo.
• Pre-commit ruff checks are passing
• Testing has been adjusted to expect the non-AssertionError error classes that will be created instead.