I'm wondering if this is an extension of uniform policy - and concerned with smart grooming and rules on hairstyles which are or are not acceptable in this particular school. The words the teacher used sound to me like a way of saying 'You ought to groom your eyebrows' , only using a more polite phrasing.
If it is natural for the hair in this child's eyebrows to stick out, why should she change it? The age of eleven is, in any case, very young to be expected to present oneself in a poised and artificial way, as she might do if she were a seventeen- year-old with a Saturday job working on a make-up counter in a shop.
Does the teacher think the child has made her eyebrows more conspicuous than usual, in other words, she is critiquing what she thinks is a vanity choice, not what occurs naturally when the hair does what it wants to do?
Surely to question or imply criticism of a natural feature is completely wrong, within this context. If your hair or eyebrows naturally grow a certain way, then so be it.
But, it wouldn't be a good time, anytime to make a teacher feel bad about a comment which, in all likelihood, was meant constructively. At the moment, especially, teachers have enough to deal with.
I would probably look at the school rules and what is said about dress, hair, grooming and makeup to see if the comment could in any way be related to this.