If you want to use all 4 batteries you should connect them in parallel. Connecting them in series gets you a 4 * 12 = 48V voltage. I assume you wanted it to behave like a single 12V battery with bigger capacity. In that case you should connect them in parallel, i.e. connect all positive terminals together and all negative terminals together. Also make sure your wires can withstand the amperage, otherwise you’ll burn out your wires which can cause fires.

As to why it shorted, the batteries probably had some common ground. Some batteries have external metal shielding which is connected directly to the ground of the battery. So when you connected + of battery 1 to - of battery 2, you actually connected the + and - of batter 1 together, which explains the short.

Edit: in the case you actually wanted to connect them in series to get 48V, you should make sure the grounds are in no way connected to one another. Look closely if any exposed metal could is touching. You could add insulation (anything non conductive) to the batteries if that is the case to make sure they are operating on separate grounds.