1. 3 of my hens have started laying in the dirt instead of the nesting boxes
How long have they been laying? Have they just started laying or has it been a while? Are those eggs randomly scattered or in one spot that is obviously a nest?
Two different things could be going on. Some pullets seem to know an egg is coming and purposely lays it where they want to right from the start. They lay it where they want to, not necessarily where you want them to. But some seem to have no idea an egg is coming. They may drop it just walking around or even from the roost. Once they gain control of the process they lay where they want to, not at random but that can take a while, usually less than two weeks. Often it takes just a few days.
No matter what, I like the idea of fake eggs to show them where to lay.
If they are dropping them at random, be patient. Try to keep all random eggs picked up so they don't think that is a good place to lay. As long as they are at random I would not do more than that.
I build some of my nests so I can lock a hen in it. If I catch a hen laying somewhere I don't want her to lay I catch her and lock her in the nest I want her to use until she lays that egg. I usually just have to do that once for her to switch nests.
A radical thought. Is where she is laying all that bad? Could you just let her lay there? Or maybe build a nest there? It works for some people but that depends on where the nest is.
2. 2 of my hens are laying in the same box at the same time. It is only big enough for one but they squeeze in together and subsequently step on at least one of the eggs, sometimes just putting a tiny hole in it or crushing it altogether
My nests are 16" cubes. It is not unusual to find three hens in one nest while all other nests are empty. It is just chickens being chickens. My eggs are hardly ever damaged. Even a hen alone can walk on the eggs getting on and off of the nest. I suspect your problems have more to do with the thickness of the eggshells than the hens laying together. When I find a damaged egg it is usually one with a thin shell.
How are you feeding them? How much calcium are they getting? Are you offering oyster shell on the side? I give mine the option to eat as much oyster shell as they want and most are pretty good at regulating that.
Is it the same hen's eggs that are damaged? If so, there may be something wrong with her.
Nothing sounds unusual but it can certainly be frustrating. Good luck!