Why do some transactions have more than one input?
What might be confusing you, and which is a common misconception, is that the addresses themselves somehow "hold" the bitcoin balances, and gain and lose the coins via transactions. In fact all the blockchain does is link up previous outputs to new inputs, and the keys make sure only the correct person is allowed to send the coins. 

Your balance is just the sum of the total unspent outputs and if you want to send a certain amount to someone, you end up creating a transaction which uses, as input, enough unspent outputs to give the right amount of coins. So if you have a few different smaller unspent outputs, and want to send a large amount, the transaction will end up using multiple of the smaller outputs as input. Because inputs and outputs are used as wholes - they can't be split up as such -
 you then usually receive a bit of change based on how much the total inputs sum up to, and how much you intended to send.

Of course, most of this is worked out by your wallet client or website which you use, so as an average user you wouldn't normally know in advance how many "addresses" are going to be involved with a specific transaction. The program will just select enough unspent outputs which you hold the keys to, and use them to create the transaction. Hopefully that answers your question to some degree.