I have a theory about the TARDIS not liking Clara that could be interesting. Theory relevant to AFTER series 7 has ended.
Suppose the TARDIS was the #305th of its make (just a number 🙂 ). The GI jumped into the Doctor’s time stream and sabotaged it. Clara jumped right after, and said “don’t steal that one, steal THIS one” gesturing towards another TARDIS. Say, #63.
So instead of stealing TARDIS #305 – our TARDIS – he steals #63 which is a completely different one. Different soul. And has all his adventures with #63 instead.
That may be why TARDIS #305 dislikes Clara. The woman who changes the Doctor’s TARDIS.
However, it’s a nice theory, but I doubt that it’s true.
(305 was chosen because that’s the number of type 40 TARDISes made. 63 after the year the show started to air)