Miku showed no confidence problems until this arc
She could face Ichika when she saw that she was being close to Fuutaro
She declared herself to Fuutaro in the livinroom, although this started as a joke and ended like that, but she could say it
During the final exam she saw that Fuutaro recognized her achievements by having the best grades, and she wanted to be the best on the exam so that Fuutaro would recognize her even more and have something that makes her special with respect to others, if you ask me I do not think that's a bad idea if you want a person to notice you
She did not succeed, and it was there that Negi used that to make her feel like a coward (ch.61).
In the scrambled eggs, she, somewhat frustrated, went to Fuutaro and told him to end their student-teacher relationship, since she could not find another way for Fuutaro to stop seeing her as a student.
Fuutaro finds her and she realizes that Fuutaro watched her enough, to the point that he could recognize her and saw that even as a student-teacher, he noticed her
With that in mind, she looked for another way to approach him and in the job interview, she remembered that Fuutaro did not dislike her food and she saw that she could use that as something to get closer to him
Now, her reaction to Ichika's actions was natural, since she treasured this moment and was exposed in the worst way, something that Negi made more dramatic and deviated from the subject, mixing her natural sadness with a distrust that arose at that moment , since she was confident of giving him her bread and when she was exposed there is no point in losing it, but if she feels depressed about it