My biggest complaint about Anomaly is the lack of Special Containment Procedures
Anomaly is often compared to SCP both genuinely and humorously, but while it nails the sterile, impersonal, and oftentimes exploitative nature in a way that many games actually themed around SCP don't, it lacks what really makes SCP interesting.
Special Containment Procedures come first because they're the most important thing to understand about actually, well, containing. In Anomaly, the gameplay is centered more around capturing the anomalies or getting rid of them, with containment appearing mostly to be an afterthought that exists for progression. There's very little depth to it and I think that's where it misses the mark the most.
I don't think that Anomaly needs to have a lot of complexity in this regard, but I think as it stands it doesn't have enough. Almost every anomaly that is containable is contained the same way, for some you can also refrigerate them too. The only real difference between containing a Gorehulk and a Noctol is the resources you get from them and how strong the walls need to be.
Even something like "the shard inhibitor is less effective on this anomaly" or "containment of this anomaly requires a psychic suppressor" would really help. Ideally I'd like each to have a small containment feature of some sort, like having certain furniture in the room or something, that you discover as you study it. Just something to make containment feel more diverse and like it doesn't quite end once you've captured the anomaly and have a plan in case it escapes.
I'm sure the mod community already has stuff in the works in this regard, and I'd do it myself if I understood the game better. I do wish it was part of the DLC vanilla, though.