iPhone 6 glass only replacement left bubbles

This machine is listed as a 2-in-1 OCA Plate Type Laminating Machine 12" Vacuum Built-in Pump and Compressor. It is supposed to remove bubbles as part of the process.

Based on your info and pic I found your machine on ebay, and according to all of that it does seem like it has a debubbler as part of the process. From the looks of the design it seems that the autoclave part has been incorporated into the vacuum lamination part, and is secured (rather awkwardly, IMO) by those four eye bolt-type pieces at the top (what they call "fixing nuts" on page 6 of the manual). That being the case, I would suspect that it's not holding a proper seal. A true autoclave uses a removable screw-on door to ensure an even 360 degree seal. Using four manual screws like that seems like a cheap workaround to me since there's a very good chance of an uneven seal. If there's a break in the seal, even a tiny one, the vacuum will pull air from that seal rather than from the bubbles in the screen (since the damaged seal will have less resistance).

Okay, so I've run the glass through the machine a few more times, heating it up on a hotplate between cycles and the bubbles are getting smaller. I think I know where are least part of the problem is coming from though. I had been leaving the glass in the mold because the instructions I was following mentioned putting the glass in the mold but never mentioned removing it or that the mold shouldn't be in with the glass. So I'm hoping my problems are due to that mistake since the videos I've watched today don't have the mold in them. EDIT: Also the seal does seem to be holding since the pressure is staying at 100 psi without the pump reactivating during the 10 minute process.

That sounds reasonable to me. When I laminate a screen I take it out of the mold to put it into the autoclave, though in my case it's because my machine has two separate places for the lamination vs debubbling process (plus the mold won't fit in the autoclave).