I would possibly argue it is ideal, even. The other two obvious alternatives is that the charity pays someone to deal with paperwork (which we wouldn't call "waste," but means even less of donations go towards the mission), or disorganized people just don't start charities and find for-profit jobs.
If you want a vibrant charitable ecosystem, letting people be imperfect about how they run their charities is a good thing.
> letting people be imperfect about how they run their charities is a good thing
I disagree - charities receive special protections and privileges from the public and in return they agree to make themselves accountable.
If they aren't making themselves be accountable then they aren't keeping their side of the agreement with the public and their protections and privileges should be revoke.
The agreement with the public includes the agreement that a missed filing results in a fine, not in revocation of their protections and privileges.
But more generally - my claim is that if the public wants a deal with charities where they must be flawless, that's a bad deal for the public. Effective people will make mistakes sometimes, ranging from missing a filing deadline to hiring people who end up not good at their job to trying some charitable activity that ends up not working. If we hold them to a standard of perfection, the rational activity of the people behind the charity is to just do something else. Is that good for us?
Of course we want them to be accountable - I'm not arguing that they should be able to do whatever, and they should try to meet all these requirements, that's why we the public encoded the requirements in the first place. I'm arguing that there's a big difference between accountability and expecting perfection.
If you want a vibrant charitable ecosystem, letting people be imperfect about how they run their charities is a good thing.