We don't know for sure.
As far as I'm aware, this is never explicitly addressed later on in the series.
However, I think we can hazard a guess based on a few other factors seen during the quirk assessment test.
While Midoriya may have performed as well or even better than students like Hagakure that gain no real physical advantage from their quirk, we have to remember that Midoriya's quirk injured him severely during the ball throw. While it was not as bad as Aizawa may have expected (just his finger versus his whole arm) it's entirely possible that Aizawa deducted points due to this injury. This is a quirk assessment test, after all, and breaking a finger after merely throwing a ball is a severe disadvantage to a quirk no matter how you look at it.
Hagakure, meanwhile, may not have had any real major advantages like Midoriya, but her quirk had no disadvantages either. I would assume she's also fairly strong herself, as mentioned in the comments to your question, so it's not unreasonable to think she had a similar (or even better) performance when compared to Midoriya in the contests that neither had any advantage in.
This would apply to the other students with quirks that do not enhance their physical strength as well, like Koda, Shoji, or Jiro, among others.
Considering that Aizawa was going to expel Midoriya before he thought to use only his finger, I'd say Midorya actually did quite well to be placed last instead.