DOJ's resources are extremely limited. They're tasked with doing for more than they have the capacity to do thoroughly.
The reason their legal arguments are sometimes strained is because they're tasked with enforcing often stupid laws on a shoestring budget. They're the ones who have to articulate to a judge justifications in terms of Congress's stupid laws.
In comparison to whom they can go up against (at least on one end of the size spectrum), and the degree of resources they can exert via other arms of the executive branch, it is probably safe to state its power is unrestricted (if not fiscally unlimited) in scope.
Well, with an operating budget of $27 billion they certainly have more resources than I have, even if they only allocate a half million dollars worth of resources (which would be about 2 people if we grossly divide by headcount, which I admit is not accurate). So I certainly wouldn't want to get on their bad side.
Also not all small businesses have resources setup to counter DOJ actions since they might not be anticipating having to until it actually happens.
2/3 of the DOJ budget is just FBI and the Federal Bureau of Prisons. ATF and DEA are also part of the mix. Actual litigation resources is only $3.3 billion, or about the equivalent of three large law firms. For an agency tasked with prosecuting everything from rapes in Indian country to to international crime rings.
I'll take at face value that trial resources are limited at a mere $3.3 billion; having the FBI investigate you and being threatened with Federal Prison time is still within the power of the DOJ. If we assume a fairly high conviction rate of DOJ cases, then it is probably not because they all ended up at trial, but because the FBI had so much on you and the threat of mandatory prison sentences so onerous that deals will be cut to avoid an expensive trial.
No one wants to go to trial, so not having a big trial budget isn't surprising; most of the hard work in building a solid case is in the FBI and the most of the leverage is in the prison system.
Please don't read into this as a condemnation of the DOJ as a body, just my take that it needs to be kept in check by courts as fighting the DOJ is not just making good show at trial.
The FBI is under DOJ, but it doesn't make much sense to lump them together for the purposes of discussion, because the FBI operates mostly independent of the DOJ (as in most governments, there is a organizational barrier between the police force and the prosecuting entity).
No doubt going up against the DOJ is not easy, but it's not exactly an organization that's overflowing with resources given the enormous scope of its responsibilities. That's why it takes such a scorched earth approach--it can't afford to spend time on weaker cases or hashing out fine distinctions in cases.
The reason their legal arguments are sometimes strained is because they're tasked with enforcing often stupid laws on a shoestring budget. They're the ones who have to articulate to a judge justifications in terms of Congress's stupid laws.