I recall several things struck down over the decades as unconstitutional when they required an individual to incriminate themselves.
If they were to prosecute for this often they would increase the chances of it being successfully challenged.
It could easily be found to violate the right of protection from self-incrimination, as similar requirements have been in the past.
Many who fail the background check are also not prohibited, just read all the stories of people that have trouble with NICS.
I imagine a large percentage of those that do fail are not really prohibited or recently became prohibited, or are only potentially temporarily prohibited (like those under indictment before they win their case.)
There is also those subject to restraining orders, state level prohibitions over misdemeanor offenses, and people that have firearm rights restored in states that allow that in a way that satisfies the feds.
The records of big bureaucracies change slowly. Someone no longer prohibited may still be prohibited in a computer for years. Weeding out real prohibited denials and fake denials would require thorough investigations.
Federal prosecutions are expensive, and they try to go after those who have assets to seize or tack on minor charges on individuals which are already being charged with something else.
Expensive prosecutions that result in minimal or no sentence at the expense of other prosecutions is something they weigh.
They have a budget for prosecutions, if they had an unlimited budget they would go after all the minor things, like FFLs that forgot to dot i's and cross t's or abbreviated X number of times over Y years aka "dozens of violations of federal firearm law over a number of years".
Fortunately they must prioritize because of budget constraints.
