The card size of the cards in the expansion are slightly larger than those in my base game.

This is disappointing as there are the new event deck cards for the new houses that need to be mixed in. The house decks, allies and reference cards are all separate and not mixed in, so this does not cause an issue for those cards.

Were there later printings of the base game with the larger card size?

Mail customer service, for a twofold reason:

a) they should be made aware of the problem
b) in case there's a problem with just your copy, they will send you replacements

Thanks Julia. As it happens I did just get a response from customer service this morning.

Quote

Thank you for your request. The compnents you show falls within our tolerance range. If you are unhappy with the quality of your components, we recommend that you return your merchandise to the retailer from whom you purchased the product for a monetary refund or exchange, according to their policies. As always, please contact us directly if you have any further questions or concerns. Thank you.

So this means that they're aware of the issue and don't consider it a problem, or at least not enough to affect game play. Something that I disagree with given that even a small difference in size is visible and means that common shuffle techniques are affected.

I agree with you on this. Possibly sleeving could help smoothing the problem?

Sorry, seems bad customer service here. It's also very odd: I've a ton of games from FFG and cards are all cut properly :/