Counting House/Council Room. I don't know what I bought them together; probably to use +buy from Council Room to buy copper ? Anyway, I played Council Room instead of Counting House and triggered a reshuffle, which is very bad for Counting House.
Another pair is ... Copper/Colony. both have six letters and start with Co-. To make the matter worse, I misread when I played Ambassador and sent my Colony away instead of Copper.
Finally, Throne Room/Trade Route. When you play multiple Throne Rooms, it's hard to keep track of how many actions you have left. I played at least five Throne Rooms and then Trade Route. Forgetting that I had to trash a card twice, I trashed Throne Room when I really meant to play it, and was confused where my last Throne Room went. The blue text for both cards are very similar (choose a card to trash/play twice : then a long list).