[chrisherring]

That thinking does help, I did read that on one of the sites as well but in some cases the capture appears to mean the loss of territory itself in addition to the actual pieces and it's hard to weigh up the value of each territory.

[Jach]

Another reason the computer might ignore a direct capture is because the stones are already "dead", it doesn't need to waste a move to actually capture them unless you futilely try to save them. Solving tsumego might help you see those cases better when it's not as simple a case of leaving your stones in atari. But yeah, even if you can "save" them next move it might still ignore the capture if there's a bigger (in terms of gaining / securing territory) move on the board, especially if your save actually isn't making them alive yet.

I think scoring and score estimating is one of the hardest things to understand (for full games I still often use a $5 android app where I just upload a picture of the board game, help it convert to an SGF, and then it auto-scores it, though sometimes it's faster to just count by hand), especially since there's multiple ways of doing it. With simple territory scoring when the game ends the dead stones that haven't actually been captured yet still get removed and added to the prisoners pile and the prisoners fill in your other territory so it might feel extra painful to lose stones... With area/stone scoring you still remove the dead stones but prisoners don't (directly) matter for the score, since you're just counting stones on the board plus uncontested area. But if a game was X moves with black having X/2 stones but white only having (X/2 - 10) stones on the board, clearly (assuming X is even and no passes, or if passes then giving up pass stones) 10 white stones were captured at some point, so there's already that relative difference in score before counting anything else. With some qualifications, the results (and the relative scores themselves) from each counting system will be the same. Thinking more about your relative score instead of giving each player actual numbers might help; I feel slightly better if I lost by 10 than if I had a negative score, say -5 to 5...