First the concrete. Any civil or structural engineer could have told them that the concrete would absorb CO2 during the time it is curing, which is probably decades. They should have at least had some quantification of how much their concrete would absorb CO2. This would have been fairly easily mitigated by sealing the concrete, ie a few hundred gallons of Thompson’s or sodium silicate, or something like it.

The compost. I know its all touchy feely and good gardening practice to use lots of compost, but say your building a Martian habitat out of metal you refine up there, and glass and concrete you make from native minerals and earth err, Mars. Where does one get compost? You don’t. The first Martian habitats are going to have to grow the first crops out of the 100% mineral soil. It can be done, that’s what hydroponics are. They shouldn’t have used any compost.
They would start making compost from the waste biomass after things were going for a while. Then the food would start tasting better, but you can certain live on hydroponic food for a while, a year or so. I think they let the horticulturists have too much say, and the astronauts not enough. If they’d have done these two things, the project would have been much more successful. I know, easy to say in hindsight.