Shield interfere with Serial Communication
You really do need to provide information on the shield, there are many versions out there (and I own half of them ). 

In essence, unless you are using an alternate serial port (SerialN) or software serial, then YES, your XBee will be using the same lines as your Arduino. If you are using Serial.print or Serial.write to talk to the XBee, then that is a giveaway too. 

The reason for this is the XBee talks to your Arduino through the serial port, but the Arduino IDE also talks to your Arduino (for programming and Serial.print) as well. You can only do one successfully. 

In answer to your second question, most likely not. It will be the XBee shield causing you your problems. 

edit: I thought I would add, I actually have ONE shield that uses RX and TX but also allows for programming at the same time. This is achieved through a series resistor and (in the case of the shield) an amplifier as well.