I fucked up, how do I fix it?

So the other night I had sex with a friend. It was good for us both or so I thought. Talking to her last night I made her uncomfortable with somethings I did and now i feel terrible. In my defense she never said she wasn't comfortable and at one point she even told me to do something but now it's a big issue.

Things i did that we're mistakes 1 Kissing 2 she had her top pulled up and it got in the way so I pulled it off 3 I was behind her for most of the night, she said she wanted to face me so after a break I had her lay on her back. She said thank you several times while like this 4 Eye contact

We had ruled things out before hand, no spitting,slapping, that kinda thing because it's not her thing but she didn't tell me anything else so I assumed it was okay. Now i feel like i violated her and feel like shit. I've already apologized but how do I make things right?

EDIT to be clear we were already having sex when this happened, both sober I'm just an idiot.