In the end-game graph it's saying my ally had more research completely than me no matter what race he was when we both maxed out our research. It's not really a problem, it's just confusing as to how he can possibly do more research than me when we both max out all our research. I guess my question is, is there some other thing that counts as "research" that isn't actually in the research (F2) tree?

TEC has more technologies to upgrade than Advent, it's that simple

He researched them before you did.

simply put advent has an ability that allows you to research atleast 33% faster than other races. Since he Finished researching before you did the graph says he did more research than you. I know this for a fact cause its happened to me while I play advent and only research like 10 things while a Vasari player researched the same amount and had less than I did.

really

thats bizzare then. I have nothing in my experience that can explain that it must be technical then.

Sorry, I misread you there.  This one doesn't make sense to me, either.  Unless you're missing something (like fleet research or maybe artifacts, as someone else suggested) this seems like some sort of bug.  Reminds me of when the end-game statistics would actually say you had a negative amount of frigates at the end if you used the illuminator's illusion ability.  Just a funny little bug, and there's probably something silly happening that's screwing up the statistics.