Too many unknowns about what actually transpired throughout the course of the meet to comment too much on this specific situation, but I'll say that gobluesasquatch offers some pretty good analysis in his post on page 4.
Sharing some general observations & info from my experience over the past 15 years of officiating and also providing the actual copy from the rule book:
As some have already mentioned, that 2:21 "split" is likely for 2 laps of running for that athlete. The splits that look "off" are likely due to the timing company either just totally missing reading the photo or not being able to read hip numbers on the photo taken for that particular lap that is missing from the split. They don't use chips on the track like in XC or on the road - they take a photo of the runners coming through every lap and have to manually mark each athlete and the timing software then generates the time for that runner.
There doesn't need to be 1000 rules for there to be a 1000 interpretations - there can even be one rule that is interpreted in different ways. In fact the rule book even admits:
Part I pg 9: "The rules are intended to provide direction and be as concise as possible. They are not meant to be comprehensive or cover all situations...the NCAA T&F rules committee recognizes that the rules are neither perfect or complete...decisions made by applying these rules and those situations not covered by these rules must be reached consistently within the spirit of fair play and safety..."
Bottom line is that our sport is a complex one and there is not " ambiguity via excessive rules." If anything there is ambiguity via a focus on trying to make the rules as concise as possible.
That is why the NCAA track & field committee issues rule interpretation documents answering questions about situations that arise - which is where the verbiage that I shared on the bottom of page 1 comes from. Not the rule book, but an interpretation document...and they aren't comprehensive either.
Moving on to what the rule book does say about some of the players and aspects of this situation...
The role of the referee as it is defined in the rule book includes:
Rule 3 Section 4 Article 2a - "After consulting with the appropriate offiicals, to take actions and make such decisions, including those for which the rules make no specific provision, that provide each contestant a fair and equal opportunity..."
The role of the athlete as it relates to honest effort is:
Rule 4 Section 2 Article 1 - "Competitors...shall be responsible for conducting themselves in an honest and sporting fashion...this includes competing to the best of the ability for a given circumstance (that is, honest effort)."
In this same section related to the role of the athlete it goes on to address "Failure to Participate" which is specifically defined as starting the competition. That obviously happened in this situation so you could argue this section isn't relevant, but I'll go ahead and quote one section anyway:
Rule 4 Section 2 Article 2d - "The referee, upon proper protest, based upon all authorized evidence and with consideration given to circumstances beyond the control of the competitor, including documented severe medical conditions, shall determine whether circumstances clearly demonstrate that a violation of this rule (failure to participate) has occurred."
So although this process is in the failure to participate section, a referee likely also uses is as guidance as they work to determine whether the honest effort rule has been violated. Meets may implement their own set of administration guidelines that dictate being treated by meet medical staff so "documented medical conditions" are consistently documented and also easier to track down by the referee. It sounds like something along these lines may have been communicated at the coaches meeting.
When I serve as a referee - especially for a multi day meet - I'm always on the lookout for DNS, DNF situations. Those are red flags and always require me to look into the situation, so I agree that was likely a missed opportunity by the referee to get ahead of a potential issue and address it before the kid was on the line for the 5k.
And lastly - the comparisons to the NBA don't make any sense since there isn't an equivalent rule to even compare, unless you want to compare honest effort in track to the no flopping penalties that are being issued these days? :)