This is wrong.

We know that either:

a) there’s mysterious undetectable particles, or

b) that something beyond the standard model is happening, as in your second and third points.

There’s a failed “prediction” that all fermions have similar mass terms, and that failure suggests either something strange (undetectable particles), something strange (fermions without consistent mass mechanisms) or something strange (novel physics).

I think that qualifies as a mystery.