Frame challenges are generally about solving problems which is not the job of a comment
I'm not going to say that frame challenges can never be part of a valid comment, but the form of a frame challenge isn't generally something that is useful for a comment.
A frame challenge is where an author answers a question in a wholly different way the querent never asked for, or potentially expressly forbade, but in a way the author feels will actually solve the problem.
A frame challenge is all about solving the problem in a different way than the author intended. But in the end, they are about solving the problem, which is not something that a comment should be doing.
Comments must work towards improving or clarifying the post
As pointed out in the Help Center text for the commenting privilege: if your comment is not making clear suggestion for improving the post or asking clear questions seeking clarification, it generally does not belong as a comment.
The comment you in particular link to (now deleted) responded to a question asking "A spell that let's you travel to another setting. Which level would it be?" with (paraphrasing since I don't have the comment text [mods feel free to edit the actual text in])
"Frame challenge: use the planar travel spell instead."
This is not working towards improving the question, it is suggesting a method for solving the issue — instead of homebrewing your spell, just use one that already exists and has an established spell level already.
If the intent there was to somehow improve the post, it was failing to communicate that and regardless of intent, was interpreted (by me and at least one other person) as attempting to answer the question. So if you are attempting to make a valid comment containing a frame challenge, you must make it clear how you are trying to improve or clarify.
Suggesting changes to questions isn't really a FC, but it is allowed
"It seems like you want to correct something but there may be a better way than you've suggested, if we knew what it was"
does not fit what I would view as a traditional frame challenge, but does in fact appear to be attempting to clarify or improve the post. Therefore it is likely fine (though without context and more details it is impossible to say for sure).
Again, I can't think of every possible circumstance, so it might be possible for an answer to contain a frame challenge in some way and still be a valid use of a comment. But on the other hand, this whole thing about categorizing a comment as a frame challenge or not is a red herring.
The bottom line is, comments won't get deleted for frame challenging alone as long as it is a clear attempt to improve or clarify the post.