why does my MCU outputs some random signals for 3s before starting the program?

Couple of possibilities, either something you've programmed onto the part is doing that, or the ST-LINK is probing the part. You can disconnect the ST-LINK from the SWDIO/SWCLK pins by removing a pair of jumpers.

If that still causes issues you need to look at what you're doing. Perhaps instrument your code so you can see via a GPIO where it is, or use a debugger where you've unchecked 'run to main()' and you step or otherwise walk the code between Reset_Handler and the point where you see 'normal' behaviour.