I have not encountered it before. I have some reflections. The short version is that I would not suggest arguing that the plan is not an ERISA plan (or otherwise disclaiming the plan, its existence or its ERISA coverage solely on the basis that the employer didn't authorize the plan), and the employer probably has some state law claims against the business manager, but frankly should be more concerned about the lack of internal controls that allowed this to happen without the employer's awareness.
@Gina Alsdorf is right, a lot depends on the facts and circumstances. As is always the case with legal questions, "it depends.'
From my armchair, between the participants and the plan, I doubt there is a valid argument against the plan's existence or contributions being plan assets. That ship has sailed.
ERISA probably preempts state law contract and agency law principles with respect to participants' claims about the plan and its existence. The mere existence of a written plan established and maintained to provide retirement benefits under the auspices of the employer, even if it was without the employer's authorization, and to which employees contributed, would likely be enough to deem it a "plan" under ERISA. Also, employees would have estoppel arguments that the plan has been held out to exist, with reliance (contributions withheld) and operated under the auspices of the employer. The employer would be on very shaky ground trying to disclaim or undo the plan and even more shaky ground claiming it did not exist or was not established and maintained by the employer, even if the business manager did so without authority. The employer would probably be inviting ERISA claims if it did so, and should prepare to pay participants' attorney's fees if it goes down that path.
To the extent state law (or federal law--courts have held ERISA contemplates federal common law contract principles), the business manager's apparent authority is usually enough to bind the employer to the participants and service providers. Unless participants (or service providers, if the employer is concerned about having to pay them) knew that the business manager lacked authority to act in this capacity for the employer, an agent's (business manager's) apparent authority is usually enough to bind the principal (employer).
Between the employer and the business manager, the employer may have a claim against the business manager for acting outside of the scope of their authority, if there is a way of establishing the parameters of the agent's authority (burden is on the employer). The question is what the damages are. I'm guessing this is a small employer and a small 401(k) with a large TPA where the fees are minimal, so below $10K/year. That is unlikely to be worth litigating over.
I imagine this is a small employer, but the fact that the business manager could set up a plan and arrange to withhold employee contributions for any period of time without the employer's awareness raises serious questions about the employer's internal procedures, oversight and financial controls. This whole situation should force some serious self-reflection on the employer's part.
(None of this is legal advice. Just some reflections to help give your reflections some structure.)