[spoiler] um...Could we not just have come back for him?

[WALP]

I'm not sure if I get what you mean, but if she really thought Simon already understood the copy concept, I'm sure she only thought so after Simon-2 was copied (because Simon-3 got to experience that in practice), so Simon-2 would still surely be confused and mad about it.

Yes but she only just saw how Simon-3 reacted to it. Sure he got mad but he could definitely deal with it, and if the option is between killing Simon-2 or making him mad as well then I think it's pretty black and white what to do.

About Simon-2 being stuck comments I think that is pretty obvious, but it does not matter because Simon-3 and Catherine could come back for him. Of course the event of Catherine's suicide busting the omnitool complicates things, but even then I am doubting that how planned that suicide was, and it could very well have been delayed so they could come back for Simon-2 first. Even given it is impossible for a scenario where Catherine does not kill herself after ark launch, it would be really weird if there was not a single corpse in phi/alpha/tau/nearby abyss carrying an omnitool, since those are required to enter stations in the first place.

In the end I can only see it being explained by simple confusion, but had they been more aware there's no doubt coming back for Simon-2 would have black and white been the best option.