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Aperture Science appears to be in the middle of nowhere, I doubt they even FOUND itMaybe they where somehow unaware of Aperture Science. It was seen to be located in the middle of a cornfield, and also the carpark at the end of Portal 1 was empty, so the combine probably thought the facility was deserted and didnt bother with it. It could be assumed that the Combine never even discovered Aperture Science, being almost completely underground and vastly hidden from outside events. GLaDOS herself hints at the invasion during the boss fight of Portal, stating "I have seen what it's like out there, and I am the only thing protecting you from them.". Also of note is that the Resonance Cascade and the Combine Invasion of Earth happened precisely three days after GLaDOS' takeover, so no-one but her would of been able to see the outside world.Well, if you play Half-Life 2 and all of the Half-Life Episode, you learn that the entire Combine army is NOT on Earth. Mostly, the Combine stationed on Earth were human-turned-Combine soldiers. This means, and this is also demonstrated in-game, that the Combine didn't really bother keeping patrols over the ENTIRE planet. This, combined with the fact that Aperture Labs is in a somewhat remote place, could mean that it was simply overlooked. Also, GLaDOS says she was "keeping them away," which could reference the Combine.They don't even know the Aperture science lab was there its all underground and plus its in a remote area so the combine have not checked there.The Combine haven't found Aperture Science. GLaDos makes this clear by indirectly referring to the Combine as "them". She also says that attempts were made to keep them out.they had already developed, and were being taken over by GLaDOS by the time of the Seven Hour War. I honestly wouldn't be surprised if the incident at Black Mesa and the One at Aperture happened at roughly the same time, maybe even helping to cause one another.

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