As long as your are not forcing unwanted contact or legit scaring here, you are fine...Are you toweling her to get her off the shelf, or grabbing her? Because that does harm trust/scare a bird. If she is stepping up and then you put her in and she's annoyed, that's fine (probably, as long as she isn't genuinely scared of the carrier, and if she is, that is something you train for gradually via positive associations and slow exposure). Another thing, try not to follow predictable patterns when picking her up (sometimes pick her up and don't put her back in the cage/carrier after she has been out for awhile).
If she is going up there and you are having to pry her down/ struggle/use force, then you need to cover that shelf or make it less appealing so that this doesn't happen whenever she is out. A slight prying of the toes w/out biting is okay, but grabbing, toweling/forcing should be avoided.
Do you let her go in and out of her cage without locking her up the second she's back in? Lots of people mistakenly shut the door on their bird the second the bird goes in voluntarily (like, "YES, GOT HER!") but that is harmful because it teaches the bird that anytime he/she enters her cage, she will be locked up, which leads to avoiding it unless they are placed in there against their will (which is something to avoid).
When you say carrier, do you mean a carrier or cage? If you mean carrier, why are you putting her in a carrier all the time (just curious). That can be scary for some birds if they associate it with the vet, leaving etc..or if it's a new and unfamiliar carrier in comparison to her cage.
Just like a kid, they will get mad about stuff they don't want to do, but the key is differentiating legitimate fear/upset from pouting because they didn't get their way.
Also-- It sounds like your bird is young, but make sure that you don't allow access to shadowy spaces in or out of the cage (huts, boxes, low shelves, under furniture, in bedding etc etc).. These will become hormonal triggers at sexual maturity (and subsequent behavior triggers), and you don't want her to get used to things that won't be acceptable within a few months. It can also be particularly hard to remove a bird from a nest-like space when they are hormonal, and that is not a fun struggle to have (and it stresses out the bird, so just telling you as a heads- up in terms of what you should be thinking about for the near future.
When you say cuddles, make sure you are only petting on the head and neck. The rest is reserved for a mate in the wild and you don't want to be perceived that way.
Prolonged petting in places other than the head/neck and access to snuggle huts, shadowy spaces etc, can also lead to health consequences in females, such as egg-laying (and potential egg-binding).