Mr. Mueller’s refusal to pass judgment on whether the president broke the law is one example of how the special counsel operated by rules ill fitted for the Trump era. He said nothing and the president said everything. He worked in secret, allowing the president to fill the void with reckless accusations of a witch hunt. His damning conclusions were encased in dense legal jargon that the president distorted into a vindication.

Mr. Mueller seemed to expect that the system would work as it had in the past, with Congress or perhaps voters making the decision about whether Mr. Trump had committed a crime, only to see the president’s handpicked attorney general — and Mr. Mueller’s longtime friend — make his own determination that there was not enough evidence to support such a charge.

Congress might still pursue impeachment, but many Democrats who oppose Mr. Trump for now seem unwilling to act on findings they have described as outrageous without what they see as explicit instruction from Mr. Mueller to do so.

“Now you have institutions talking past one another,” said Matt Jacobs, a lawyer at Vinson & Elkins who worked for Mr. Mueller as a prosecutor and a spokesman. “You have Mueller thinking he was very clear in providing evidence that others can pursue. And you have a Congress that hasn’t shown itself to be capable of untangling the evidence.”