Didn't the WOs have senior officers?

They would have had superiors, but Warrant Officers are accorded military courtesies usually observed for Officers, yet they are enlisted personnel. They only appear in highly specialized or limited MOS's, though, and are somewhat apart from the regular structure of things. They rank above all enlisted personnel, and above Officer Cadets, but are still ranked below an O-1 (2nd Lt.)

In the book there were several senior officers from the CID. From the 2 I remember one was their superior Colonel from CID headquarters, the other one a Major stationed there.

While Warrant Officer are ranked below 2Lt they are not all really treated that way. WO1 and CW2 are mostly equal to LTs and CPT (company grade officers) CW3 and CW4 are treated about the same as MAJ and LTC (field grade officers). A CW5 is very senior in the Army and gets treated as a COL.

While a captain out ranks warrant officers, he would treat a WO1 or CW2 basically as an equal and call them by their first name. He would treat a CW3 or CW4 very differently. He would call them Chief and have a lot of respect for their knowledge and ask them for guidance.

It is not unusual for the Army to use CW3 or CW4 investigators in cases involving officers all the way to COL and possibly generals. In cases involving generals, the warrants are involved but usually do not talk to the general. Actual discussions with a general under investigation would probably be done by a COL or general.

In the US Army, few of any rank are dumb enough to interfere with a senior Warrant Officer doing his job. These are commissioned officers just as are lieutenants and above, except that they are highly qualified and specialized professionals who, unlike captains, majors, etc., remain in their fields for the length of their military careers in competition with contemporaries in the same field. These people really know their stuff. Generally, captains, majors, and above, command units, while warrants usually do not (but in some unusual cases can). The majority of warrant officers in the US Army are helicopter pilots, but they also fill a wide range of other specialties, and very many today do have university degrees.

With Regular Army Warrant Officers in MP (CID – Criminal Investigation) or MI (CI – Counter-Intelligence), it's the badge and credentials (B&Cs) that talk regardless of whether he or she is wearing civilian clothes or military uniform. The B&Cs are authorized and signed by the (civilian) Secretary of the Army. (The other military services have similar specialized services, such as the Navy-Marines NCIS.) Senior Army warrants in CID and MI can and do talk to anyone in the military of any rank just as do senior police detectives or FBI agents talk to civilians of any rank, and with similar authority. Note that when this film began, the warrant, who was working out of his HQ in Virginia, was under cover as an enlisted man, but he had first touched base with the local post MP (Military Police) commander (who knew him personally). The female warrant also exercised her unquestioned B&Cs authority in the men's locker room at Ft. Benning.

Those warrants who advance in CID and MI know the grey areas and boundaries as well as how far to go if their case is not solid. In both the military and civilian worlds, over time, one's personal reputation speaks volumes. Note that the three-star general in this film first met the CID warrant when the former was a captain and the latter a private – both serving together in combat in Vietnam. (You can also read this on their uniforms.) That, too, says something, including mutual respect, as the general was quick to address the warrant by his first name (Paul).

In the end, the warrant officer did his job – both as a cop and as a soldier (and as a man of ethics), despite the long personal history there. This warrant cop didn't stop even with potentially the next Vice President of the United States, a man he had long known and respected. That's what he's supposed to do. That's why he carries those B&Cs (and the sidearm). In some military situations, rank (or friendship) cannot be allowed to get in the way of doing the right thing; everyone must know and accept the need to "speak truth to power". (It's also a good idea to really know what you're doing.)