For one, pacemakers have to enter the race and start the race with him. You can't have pacemakers enter partway. They all have to be eligible to hit the record too if they are capable. Per IAAF rules, pacemakers are basically just competitors that you pay to go out too fast and drop out partway.

Also just not a sanctioned course, not proper testing protocol for doping, not open to other competitors, and so on.

(Former USATF apprentice official, though stopped officiating once I started grad school)

The article mentions “Not open conditions”. Other words, this course was chosen for the record.

Also, per the linked Wiki reference “and meet other criteria that rule out artificially fast times produced on courses aided by downhill slope or tailwind.[8] The criteria include:

"The start and finish points of a course, measured along a theoretical straight line between them, shall not be further apart than 50% of the race distance."[6] "The decrease in elevation between the start and finish shall not exceed an average of one in a thousand, i.e. 1m per km."[6]

I don't think the course itself breaks any criteria. It was just a big loop, so any slopes or tailwind would not help the runner. "Each lap of the course featured two 4.3-kilometre (2.7-mile) out-and-back stretches... There is only 2.4 metres (7.9 feet) of incline over the entire route."

https://en.wikipedia.org/wiki/INEOS_1%3A59_Challenge

The fact that bottles were handed to him by a cyclist instead of picking them up himself is one of the issues

Because the pacemakers rotated, they weren't the same all of the way through.