It does appear that the old finish is chunking up and coming off with the ecofinish. The epoxy that is applied forms a mechanical bond between the ecofinish and the original pool surface, and it has to be done prior to installing ecoFinish which it appears was done. Once the ecoFinish bonds with the surface of the pool, then if any marcite/previous finish pops off as it appears it has in the photos that would be a somewhat unfortunate but normal issue with an older pool and it appears what is happening in your situation. The only remedy that could have been done to further prevent this would have been to remove the top layer of marcite/gunite of the pool, had it redone and then put ecoFinish over it, which would have added a considerable cost to a renovation – and is something that can be done but isn’t mandatory before an ecoFinish surface is applied.
The line you copied from the ecoFinish site applies to a surface where ecoFinish has already been on the pool – as long as the ecoFinish is still there epoxy doesn’t have to be used again because the old ecoFinish can be heated and the new layer of ecoFInish put right over it – if a color change is needed or if there is a spot that just looks blotchy for instance.
It looks like the contractor is correct – the ecoFinish bond with the pool was done properly and the original plaster is chunking off – which of course includes the layer of ecoFinish as well.