Since the episode discussion threads are being flooded with theories about this, I think it's time it got a thread of it's own to relieve some pressure. Please feel free to add more theories and dismiss or validate other theories.
So far the main theories are:
1. He got it from the pit when he almost died/turned in to a hollow.
2. Rukia trasfered it to him when she gave him shinigami powers.
3. He is a reincarnation of Kaien which was turned in to a hollow before he died.
4. His own shinigami were a hollow hybrid to begin with and got unlocked along with his shinigami powers in the pit.
5. He inherited it from his mother and/or father.
6. Urahara advertedly put Ichigo in the pit knowing it would make him into a hybrid hollow.
7. The hougyoku affected Ichigo's own shinigamai powers when he was around Rukia not when she transferred her powers.
8. A combination of 3 and 5. One of Ichigo's ancestors is the reincarnation of Kaien.
9. A modification of 1. The hollow Ichigo turned up to stop him from becoming a full hollow so he wouldn't lose his host.
10. An extension of 4. The hollow couldn't take over because Rukia's powers where somehow surpressing him.
My theory:
The hougyoku within Rukia didn't affect Ichigo directly in the shinigami transfer. Since they were Rukia's powers they might have gotten immune to the hougyoku or something. But maybe Ichigo's own hidden powers were more susceptible and when he spent time with Rukia they gor more and more corrupted. Much like the way Ichigo leaked powers to others he might have absorbed the hollow powers from Rukia. So in the pit when he almost died the hollow came out and saved him, like it has done numerous times since then.
Optional addon to my theory:
Rukia was also very close to Kaien and spent alot of time with him. And if Ichigo is the reincarnation of Kaien or somehow otherwise connected to him, this might have some significance as well. Maybe because the soul got exposed in both the spirit world and the real world it had some kind of extra influence.