If I am to give my personal opinion, I clearly think its a plot inconsistency. But I'll try to salvage it just as Stephenie Meyer has done.
In the books : Twilight Breaking Dawn, Chapter 31 Talented
The following is an excerpt which takes place between Bella, Edward & Eleazar
“A very talented family, A mind reader for a father, a shield for a
mother, and then whatever magic this extraordinary child has bewitched
us with." ~ Eleazar
“Excuse me, What did you just call my wife?” ~ Edward
“A shield, I think. She’s blocking me now, so I can’t be sure.” ~ Eleazar
“It only works with certain things. My head is sort of… private. But
it doesn’t stop Jasper from being able to mess with my mood or Alice
from seeing my future.” ~ Bella
“Purely a mental defense. Limited, but strong.” ~ Eleazar
You can read the chapter summary here
From Stephenie Meyer
She has been asked this question. Specifically,
How come Alice and Jasper can affect Bella with their supernatural
powers, but Edward and Aro and Jane can't?
To which she answers
This question comes up at every single signing! The answer is
explained in Eclipse, but I'm going to tell you all anyway, just so
there's less confusion.
Bella has a very private mind. She can't be touched there. What Edward
and Aro do is clearly a mental thing; Jane, also, works inside the
head (Jane doesn't actually inflict pain on anyone's body, she just
puts the illusion of pain inside her victim's head. It's a very
effective form of torture). Conversely, what Jasper does is no
illusion. He affects the physical body, slowing the pulse and upping
the endorphin levels to calm someone, for example, or raising the
pulse and pumping out the adrenalin to excite them. Alice, also, works
outside the mind in the realm of possible realities. She doesn't see
the thought process behind the decisions, just the outcomes.
I found this answer from Meyer here. It's listed as official website of Stephenie Meyer but I dont know for sure. But her answer makes sense, albeit retrospectively
So to salvage by (unfortunate) fandom, I can draw the following conclusion
Objectively & scientifically, emotions trigger the secretion of hormones. But emotions start from the mind. Eg, fear, nostalgia, happiness begins in the mind which secrets the hormones & the entire body feels it. But I want to believe, for the sake of being an unfortunate Twilight fan, that Jasper can control the secretion of these hormones without the trigger from the mind. Thus, in the series, Bella's mood is controlled by Jasper but she is able to feel that her mood is being manipulated as her mind hasn't triggered those moods