Perhaps with the destruction of Gallifrey and other Tardis's. The Doctors Tardis is now using the entire pocket universe including the Eye. It could have been there was only one pocket universe but it was divided up between other Tardis's and Gallifrey thus giving each Tardis finite size to use. With Gallifrey and other Tardis's now gone, the Doctor's Tardis expanded to take up the whole pocket universe space, and is now seemingly infinite in size and contains the Eye since Gallifrey can't anymore.
Infinity minus infinity is still infinity.
I think when he said the TARDIS is infinite he wasn't talking about it's physical size. That would make no sense.
More like that the TARDIS can always add another room an infinite number of times but at any point the total number of rooms would still be finite and countable in theory.