She may have been scared. On the other hand she may just have the kind of personality that doesn't like being confined. Cats don't measure affection in the same ways we do, and they have many different, subtle ways of showing their love for us. We sometimes feel that doesn't measure up to our expectations. Often, for cats, just "hanging out" in the same room as us, is their way of showing they love us.
You could try to keep picking her up briefly, and putting her down again after a couple of seconds, to show her that you won't impede her desire to have fun and explore. You can also make sure you're available when you see her begin to look tired, picking her up then, and popping her on your lap for a cuddle, but letting her go if she wriggles or wants to move away.
But, you may also have to accept that she may not like or enjoy being handled too much, and settle for interacting with her through play instead.
![Hug :hug:](https://www.purrsinourhearts.co.uk/Smileys/purrs smilies/hug.gif)
Bonnie sounds like she's displaying traits of being an Alpha personality (not to be confused with Alpha status in dogs or wolves - it's an entirely different thing in a cat). She wants to be out and about "doing" and exploring, and making her presence felt in the world.
This is why many of us were commenting that it's difficult to tell with kittens exactly what their "finished" personality will be. Personally, I'd just continue to have fun with her and enjoy your little bundle of energy. I'd be celebrating the fact you're doing so well with her integration, rather than fretting about what she may or may not become.
We've had five kittens since 2012, and each one of them shaped up to be entirely different characters and individuals. As long as they're happy, that's the main thing. (Just like having kids I guess? Childless of Northumberland)
![Evil Laugh :evillaugh:](https://www.purrsinourhearts.co.uk/Smileys/purrs smilies/evillaugh.gif)