I agree, space and boredom are likely your problem. The coop is big enough for only one standard chicken, so if you could somehow turn the current run into a sheltered roosting space it would help them spread out at night if they wanted.IMO it's a space/boredom issue above all else. Your run is barely big enough for 2 birds and certainly doesn't have space to add clutter and enrichment items https://www.backyardchickens.com/threads/a-cluttered-run.1323792/page-6#post-25037140 to curtail behavioral issues. A little free ranging does not make up for them being closed in most of the day.
Can you let them free range all day instead? If not, the other option is to add a larger additional run. If you have the space I'd recommend 10x10 at a minimum (and then just place this whole unit inside the new run) because even with only 3 birds, clutter takes up space.