In the book, she was already inside Shell Cottage in bad shape from being tortured. Essence of Dittany doesn't heal everything. Dobby died very quickly. In the film, there was nothing she knew how to do. She was not a healer. She told Harry that she couldn't do things for Ron when he was splinched because she was afraid she'd make things worse.Dobby's wounds were too serious. Ron's earlier splinch was not as damaging as a knife in the internal organs. SImilarly, she was not able to save Snape.I would suppose because Bellatrix's knife had stabbed Dobby, some of his internal organs may have been damaged as well. When Ron splinched himself that was basically like sustaining huge cuts such as when Draco had Sectumsempra cast on him, which can be easily healed. By the time Harry, Dobby, and the others had arrived at Shell Cottage, too much damage had already been done and Dobby was beyond help. That's just my theory, anyway.She probably could, but she didn't because everyone was shocked. She was tortured, transported to a place she didn't know, and finds that a very helpful person has been stabbed. Once she gets over the shock, It was probably too late.Because She Didn't Have enough heeling potion Because she had her bag taken by Bellatrix back at Malfoy Manor Possibly, Hermione could not heal Dobby because the wounds he sustained was fatal Because Dobby injuries are already very fatal, and nothing can stop that. You can't stop death. You can delay it, but not get rid of it entirely
I think the book said something about her leaving her bag at Malfoy Manor, which had her Dittany and everything in it, and she simply didn't know a healing charm powerful enough to fix a wound like that.
In the book Hermione stuffed the beaded bag in her sock to save it. In the film, the snatchers got the beaded bag.