I ordered my copy from amazon around christmas and spent about two weeks painting the figures. Last night I went to play with my fiends and I noticed I was missing the "basement" tile. Going through everything and watching an unboxing video I noticed I was also missing the lock puzzles. Both the bar and cross starting pieces as well as the room piece, all located in the same punch tile. I have already bought all 3 POD expansions  as well as forbidden alchemy which I am also missing pieces from. What do I do?

 Email FFG and give them a detailed list of your missing parts. The rulebook has a listing of all of the parts that are supposed to come with the game. Any issues I've had with my games have all been resolved to my complete satisfaction. 

I sent an email,

On further investigation I have noticed I have 7 medium tiles (one duplicate), and 9 small tiles, (two duplicates). but I am missing the all important basement medium tile, as well as the components for puzzles 4a, 5a, and 6a. all the "lock" puzzles. can anyone confirm that these are all on the same punch card?

You can see here the exact list of elements. You can see what you have duplicated and what you don't have

boardgamegeek.com/file/download/70r6bognx4/MM_Component_List_detailed_v1.1.pdf

i recommend you to revise all, even wound counters

 Customer service called me and they are sending me the missing sprue

 It happened to me too. The only difference is that I live in Brazil!!! I sent an e-mail yesterday and I'm still waiting for a response. I hope to recieve the punchboard that is missing soon... Can't wait to play!