ERISA provides (and, although I readily admit my lack of expertise in this area, I have to guess that so do most states' laws provide) civil penalties for a participant to recover against a fiduciary in the event of a breach of their fiduciary duty. However in a plan that covers only the owner of a company, the fiduciary and the participant are typically the same person. I struggle to imagine any scenario in which a person would be inclined to sue themselves. In the case of a plan which covers, for example, two or more partners in a partnership (and no employees) then I could see a potential issue, but even then you have one partner suing another which is likely to involve much more than just the retirement plan.
I am curious about what sorts of situations you had in mind when you posed this question. As I said, my knowledge of states' fiduciary and trust law is very limited so it's entirely possible there is some subtlety I am missing.
Regarding prohibited transactions, a 401(a)-qualified plan is still subject to Code section 4975.
For what it's worth, I have never had the sponsor of a plan which covers only owners ask me about fiduciary issues (although I have had a number ask me if a particular action would be a prohibited transaction...in those cases, if they have to ask, the answer is usually yes).