I am sorry but I cannot see any holes in the picture you sent of the coop. Maybe you could mark them on the photo and re-post. Generally you want to have any hole larger than 1/2" covered because there are some predators that can fit into some small holes. But it looks like you are in a city so you may not have so many of that kind of predator - but even so I would not leave a hole more than 3/4 an inch without a wire barrier. Also, for proper ventilation you need very big holes - not even holes but big 'gaps' at the top of your walls running almost the full length of the wall - and those definitely need to be secured with wire/hardware cloth.
It is hard to be 100% sure. It is better that they are in the run than in the tiny coop. And the run itself is also tiny. You should look at it very carefully and see if some other animal could get in and attack them. Put your self in the mind of a hungry predator and see how you would break in! When you can't figure out how to break in you are probably going to be OK.
Finally, I really, really think you need to look at ways to increase the size of the run. It is way too small for the number of chickens. You don't need to do that immediately (unlike the ventilation and the run security - both of which are urgent improvements), but for your hens to be happy and healthy they need more space even when you can't watch over them free-ranging.
Hope that is helpful.