If he placed the liner~ getting it situated while the first couple inches were introduced & the remainder of the water came in by hose with folks playing in it ~ I personally could see validity to his statement.
If he placed the liner ~ getting it situated while the first couple inches of water were introduced & the remainder of the water came by delivery truck with a disperser and no one was in the water I feel it would be very difficult for the liner to slip on a full pool. In saying that though I am the mom of two boys in their 20's now and while growing up the whole neighborhood was with us more than they were at their own homes... I am a firm believer anything can happen. Is it likely No, but I won't rule anything out.
I don't think without knowing the whole story anyone is able to really answer this question. Even if all details come out at that point a person can only comment on the likelihood. With no info on the installer, the cove, the method of filling it's too difficult to say what actually happened. I take it this is a liner replacement because you mention it's a new liner, but made no mention of it being a new pool, that comes into play as well. I really make an effort to try daily not to be so eager to "blame" someone or "something" & realize not everyone is out to get me.
Obviously you are frustrated with end result and that is truly a shame, but I would try to keep a level head and rationalize with him for resolve so that it can be fixed to your liking. He is acting as if he is willing to work you by saying he will drain the pool and try again, he is obviously willing to try and satisfy you ~ that says a lot to me and I notice that has kind of been overlooked.
Did you sign off on the liner install when he finished and were you satisfied or did you just sign because you were excited to be done and swimming? If he did present signoff paperwork did you read it and discuss it with him prior to signing so you were clear on the info you were agreeing to?
Two weeks lapsed and wrinkles appeared in a full pool. A gallon of water is heavy (a smidge over 8 pounds) ~ there has to be a reason why it held shape intially and then two weeks pass and it's wrinkled.
Why does he feel if he drains and resituates it ~ it will happen again? Is it because of the liner chosen, the way the pool is set up or because fill water is coming in slowly allowing the sides to blow around as it fills and everything to shift around? Or is it because as it fills folks are in it cooling off and playing? Ask his specifically why it will wrinkle a second time so you know if you should go through the efforts again?
You have a contractor willing to work with you ~ if you handle this methodically eliminating factors that allowed it to wrinkle the first time (if they happened due to circumstances that can be eliminated the second time) this should turn out just fine for you. I would at least give the guy some credit for his willingness to please you and work with him through this.