For anyone wondering why Judge Kimba Wood didn't take Michael Cohen's plea, she has Cohen v. U.S., Cohen's request for a TRO to protect his docs. Judge William Pauley has U.S. v. Cohen, the criminal case against Cohen. Separate cases, separate docket numbers.
I believe that SDNY local rules do allow for a criminal and a civil case to be "related," but the judge in the earlier case has discretion over whether to accept the new case; see https://digitalcommons.law.lsu.edu/cgi/viewcontent.cgi?article=1115&context=faculty_scholarship …