The New Oxford American Dictionary (Mac OS X’s Dictionary):

noun, Ecology
a biological community of interacting organisms and their physical environment.

And the Wikipedia article, Closed ecological systems:

Closed ecological systems (CES) are ecosystems that do not rely on matter exchange with any part outside the system.

I’m going to pick on Chris Foresman at Ars Technica, although he isn’t the only offender. In Is Apple ready to play cat and mouse with malware developers?, Chris writes:

iOS is essentially a closed ecosystem, where software can only be installed via the App Store.

This sentence could be replaced with ‘On iOS, software can only be installed via the App Store.’, which conveys as much meaning as the original.

I don’t understand the analogy anyway. You can put applications in the App Store, so it clearly has inputs. This means it is not technically closed.

This analogy has gone too far. Software platforms are not ecosystems.