When you download a program to a processor, you also download the tag data stored in your offline project. If for instance, your motor is started by a boolean tag called MOTOR_START, and your offline project has a 1 in MOTOR_START's value, and there is nothing in your logic to write a zero to it on startup, then scenarios like this will happen.
When you're programming it's best practice to use the first scan bit to initialize your program, shut off any outputs, reset counters and timers, etc. I'm guess what happened is that you uploaded the program while it was running, so when you download, all the tag values will be at the same state the machine was when you last uploaded.