Mr. Bragg was not the only one to question the strength of the case, the interviews show. Late last year, three career prosecutors in the district attorney’s office opted to leave the investigation, uncomfortable with the speed at which it was proceeding and with what they maintained were gaps in the evidence. The tension spilled into the new administration, with some career prosecutors raising concerns directly to the new district attorney’s team.

Mr. Bragg, whose office is conducting the investigation along with lawyers working for New York’s attorney general, Letitia James, had not taken issue with Mr. Dunne and Mr. Pomerantz presenting evidence to the grand jury in his first days as district attorney. But as the weeks passed, he developed concerns about the challenge of showing Mr. Trump’s intent — a requirement for proving that he criminally falsified his business records — and about the risks of relying on the former president’s onetime fixer, Michael D. Cohen, as a key witness.

Mr. Cohen’s testimony, the prosecutors leading the investigation argued, could help to establish that Mr. Trump was intentionally misleading when he exaggerated the value of his properties. The financial statements Mr. Trump submitted to banks to secure loans — documents that say “Donald J. Trump is responsible for the preparation and fair presentation” of the valuations — could also support a case.

Mr. Bragg was not persuaded.