Welcome to the Forum!

Despite your claim that there is good drainage around the pool, unfortunately, it seems obvious from your description that there IS a drainage issue. (I know this isn't your fault!)

It sounds like water is running under the shallow end [my reasoning- the shallow end floats (causing the wrinkles) and it takes more than 3 years for a small stream of water to wash the cement out of vermiculite, leaving it 'mushy' or simply washed out)]

You said
as the pool is pretty high on my lot and the drainage is good all the way around it.
- how high is your lot, compared to the surrounding lots?

BTW - even a crease (wrinkle) in a 2 year old liner should come out (as long as the liner wasn't severely chemically abused).

Where are you located?

I'll try my best to help you with this