IanWorthington:
If they were told to, due to an emergency aircraft diverting to Madellin - forcing a hold - which appears to be the case.
There's some confusion as to whether or not the other flight had declared an emergency or not, but timeline-wise (in the link to the avherald article I posted above) they were cleared and entered the pattern immediately after the Avianca flight successfully landed, so I'd assume they have to be related. If ATC asked them to hold, it probably doesn't matter if the Avianca flight was "emergency" or not, it appears to have still triggered the hold for the accident LaMia flight.
The en-route alternate / diversion idea is interesting, but this is a classic example of why it wouldn't work. That scenario seems purely based upon some sort of weather delay or diversion, and would never account for unforeseen issues like a temp. hold at final destination - by then you'd be unable to divert, right? (obviously in this case, but I meant in normal ops in more typical situations and locations as well?)
Still, going bingo fuel in a 6 minute (or whatever it was) hold (after a normal, direct flight) is obviously criminal, and some hugely important rules and regs had already been broken by then.