Yes, it really bugged me that no reason was given for Ruby’s absence. She just wasn’t there, and the others didn’t question it. Realistically, she would have been in all those scenes…comforting Belle at the diner in 3×7, with the whole gang when Pan’s curse was arriving, standing at the town line. They could have at least given a throwaway line explaining where she was or had her there in wolf form.
Or they could have used her fill in good grief Ganny had to hunt down where Henry was when it should have been Red.