It depends on your camera and model, and what software is in there.

What I have seen with multiple camera models, and that is probably what happened for you too, is that they use the following algorithm:

• The camera counts internally from 0001 to 9999, and names the pictures accordingly. After 9999, it simply goes back to 0001; it puts it in a separate directory, but when you copy them together, there is no more difference between the first set 0001 and the second set 0001.
• if you use a memory card that already has pictures on it, the counter jumps to the last written picture (highest number), and continues after that. So if your camera is at 2000, and you insert a card with a picture numbered 5668, the next shot will become 5669, not 2001 (even if 2001 would be free).
• if you use multiple cards and each one has already collected some pictures, you can quickly get a complete mess...

There are multiple ways to handle that, and each one has its advantages and disadvantages. Here is my approach: I use only one card per camera, and whenever I download the pictures, I leave the last (highest number) on it, so thecamera continues counting there. On my harddisk, I add additional digits to the four digits that the camera provides, so my pictures are named '6D-0010001'; I use a small renaming tool to rename all files immediately accordingly. As I said, there are many ways, and most people will not like my approach. I recommend you make a plan for yourself how to organize it - unfortunately, you need a plan.