Yeah it would be nice if the game told you WHO won the game and what kind of victory they achieved. But if it helps you feel a little better I can give you some possible scenarios as to how you lost, based upon the information you have provided.
1) One of your allies achieved and Alliance Victory. You said that there was one faction left that you were not allied with. It is possible that one of your allies had allied with all the other factions plus that ONE guy that was not allied with you.
2) One of the factions achieved an Ascension Victory. This one can be sneaky because there is no easy to see ranking showing who has the most Ascension points on all the the normal power ranking menus. There is a menu from the govern screen where you can see a graph showing how many Ascension points each faction has, but it is kind of a hidden away chart many people probably haven't noticed.
3) One of the factions achieved a Research Victory. I believe your "research score" ranking is determined by your total number of research points generated. It is very possible that you can research many more techs than any other race, but if somebody makes a bee line straight down the research victory tech lines (ignoring other "fluff" techs) they can beat you to a Research Victory.
4) Influence Victory. When factions start surrendering, it can make all of the stats for the absorbing faction start to skyrocket. If all those factions you saw surrendering were being absorbed mostly by one other faction, then that absorbing factions influence, research, and all other "measurable" stats would start going up rapidly.
5) Turn limit victory. If you left the option enabled that ends the game after a certain number of turns, then one of the factions that had been absorbing those surrendering factions could have skyrocketed their total score up quite a bit right before the game hit it's max number of turns allowed.
Those are some of the ways the AI could have ended up winning. My hunch is that you got beaten by the Conquest/Alliance victory condition, since you said that you noticed a lot of factions surrendering and there was only one faction left that you had not allied with.