After getting more experience against some good players, I can tell that she's going to have issues against the following:
Raiden
Scorpion
Jax.
Sub-Zero
I'm not just going by 1 or 2 variations. I'm talking all of them. All 4 of them have the frames to where she doesn't want to be in their faces, but that's not why I think she's going have issues. It's the fact that they have ways to bypass any kind of range game right that instant. Mileena has a certain comfort zone that she has to play & it's not at the back of the screen. It's just in character length (sweeping distance). From there, to just right outside of it, but she also doesn't want to play in your face.
Scorpion's footsies are amazing. They are a lot better than what players believe. Just like Mileena, he plays right within character length for the most part, but he's wanting to be upclose more than playing back off of people. He wants to use D1, D2, D3, & D4 to get his advantage & then pressure. If he's not D4 range, his F3, B3, 21, & B12 are whiff punishers that can be cancelled into combos. B3 in general is a starting low mixup string, which is awesome in this game.
Most of Scorpion's players are going play Inferno & Hellfire. Hellfire he doesn't have as much in range, but he can chuck his fireball out to test your response. He has his teleport to keep her in check, but of course it can be baited into a punish. However, that's easier said than done because he can also delay the teleport & then block your reaction to him getting to the other side of the screen after you've recovered from throwing a sai. Also, keep in mind that just like his teleport "can be baited", so can Mileena's sais. The teleport punch will punish her for throwing them carelessly.
Another thing that will punish Mileena is his leg takedown. So if she's throwing a standing sai, then expect to be taken down with BF4, which is also a whiff punisher (just not as good as the other options since it's riskier). Another thing that you will have to watch for with Scorpion are his hellfire, & his minion tools. Hellfire is not blockable, but Minion grab is. If you duck or jump, then he's hitting you with his minion drop. If you stand still, he's going to find a way to hit you with his charging minion. Now he doesn't have to land a hit on you. He just wants you to respond to it, run in & then come & get you. She does have ball roll to keep him in check, so he'll think twice about doing it. Sais as well, but he will find a way to come & get you is the main point. Whether it be him coming in after you respond or be using his teleport & having to delay it.
I'll explain the other's later on. I didn't want to make a TL;DR post.