Yeah, I didn't play the game but just watched the original FSN anime and I was pretty damn confused.

There's so much I'm confused about. Like how did Berserker get owned by Gilgamesh so easily? His puny fodder weapons pierced his skin when nothing from Archer could even scratch him. Also, what's the deal with Ilya's heart? Or why were Emiya and Archer Emiya called fakes? Why did Saber disappear at the end? Does destroying the Holy Grail "reset" all the Servants?

Or how Lancer stayed alive after the order was to kill himself. That aside isn't the Servant supposed to disappear when the Master dies? Kirei dies, but Lancer stayed around long enough to chuck a spear at Shinji.

Pretty confused yeah, but it really does seem like the movie should be for you if you've played through this arc in the game.