Just had my siding and roof done...?

Yes you should say something. If you bought the materials, they should belong to you. If they furnished the materials and you were paying them for them, that would be different. If you have to replace any siding in the future it would be good to have the extra and unopened bundles or boxes usually can be returned to the store.

Sounds like the you paid for a roof and siding job and gave them money up front to help them buy materials. If the job was a contract price, lets say $5,000 and you gave them $2,000 for them to buy the materials, then it belongs to them. You bought a job done for a set price. Sounds like they would let you have the material for a fee , which would be fair.Imagine this: they finished up the job today and were short on material. Would you feel responsible even though you contracted for a set price? Certainly not. Likewise in this situation. The flashing however makes for an odd twist. If it is as I stated above then they should have bought the flashing themselves. If on the other hand you contracted them for labor only, then they owe you the material. If this is the case contact them and expect a refund for the material. If they do not cooperate, see if your state has a licensing division that regulates this type of work, and if so, file a complaint. I guarantee you this will get their attention. If the amount of money is minimal, then maybe just forget about it and enjoy your new roof and siding. (I have been in the construction industry for more than 24 years)

Read your contract. There is always an item that states that overages belong to the roofer, siding people, etc., unless you change it before you sign.