In the courts, presumption and deference rule. A person is always presumed innocent. If the prosecution can provide at least a minimally logical case, backed up by even minimally acceptable evidence (a "prima facie" case), a prosecution can go forward. When suing a federal agency for misinterpreting the law, the courts begin by presuming the agency made the right intepretation; it's up to the plaintiff to prove the agency wrong.
This last point is really important. Under federal law, regulations must be adopted according to the procedures outlined in the Administrative Procedures Act. The APA requires that a "notice of proposed rulemaking" be published in the Federal Register first. This notice requires the agency to tell the public (a) what legal authority gives it the right to make a rule; (b) a description of the problem, and the proposed rule to solve it; (c) an outline of the timeline the agency will follow in seeking comments and writing the rule; (d) how long the public has to make initial comments; and (e) how comments can be made (in writing, in person, and in other ways). Sixty days must be allowed for initial comments to be made. Thirty days later, the agency is required to republish the proposed rule. At this time, the agency must publicly describe all the comments it has received (it can lump them into groups), respond to them using logic and evidence, and must revise the rule in places where it cannot defend the rule. The vast majority of rules are revised, often substantially, in response to these comments. The public now has another 30 days to reply to the revised rule. After the second public comment period closes, the agency has 30 days to promulgate the final rule. It does so by publishing the final rule in the Federal Register for the public to see.
How much deference should courts give to this process? A lot, it turns out. Courts have done so ever since the 1880s. In 1984, the U.S. Supreme Court formally adopted this long-standing deference in Chevron U.S.A., Inc. v. Natural Resources Defense Council, Inc., 467 U.S. 837 (1984). In Chevron, EPA Administrator Anne McGille Gorsuch Burford issued regulations relaxing oil refinery admissions standards. An environmental group sued. But the Supreme Court said that, so long as the agency had followed the APA and had a "prima facie" case to support its decisions, great deference should be given to the agency's interpretation of the legal authority giving it the right to act (or not act). Only clear evidence to the contrary should be allowed to overturn an agency's decision.
Actually, agency decisions are overturned all the time. Agency's often try to slip one past the regulated entity (whether the public, a company, a practice, or whatever), and courts often slap them down for not using logica and evidence to support government action.
On January 11, 2017, the House of Represenatives passed the "Regulatory Accountability Act of 2017", which would overturn Chevron. This means that trial and appellate courts would have to look at lawsuits against government action "de novo" (as if anew), and give no deference to the agency's evidence, logic, or decision.
This puts the courts in the role of policymaker and rulemaker -- even though the GOP has often decried that.
Moreover, Neil Gorsuch -- whose mother, Anne, led the EPA under Ronald Reagan -- opposes the Chevron doctrine, and has openly called for the Supreme Court to overturn it.