Well it was technically a mistake to try and kill Fajo. He decided that Fajo was worth less than inevitable future lives (he wouldn't kill Fajo in retribution for the one life he already took, but he would as a last resort to protect others), and he needed to die. As soon as the Enterprise arrived, it became clear to Data that he was mistaken in his conclusion that other people would inevitably die.
It was a perfectly reasonable mistake, reached through sound logic, but it was still a mistake and he'd like to take it back if he could. Fortunately for him, the absolute finality of his decision happened "during transport", so no harm was done. It's one of those rare occasions where he can take back a mistake.
I think the problem is that wanting to take back his decision implies a level of emotional response Data isn't supposed to be capable of. Regret is not something he should be able to have.
However, this is such a common problem for Data plots (and Spock plots before him, for that matter) that I don't think it makes sense to nitpick this one in particular. If Data were as emotionless as he's supposed to be it'd make it almost impossible to relate to him.