Yes. Every real source has an internal resistance. Small batteries or cells have considerable amounts.
Two easy ways to work around this issue:
1: use a diferent battery to supply the motor and electronics. That way a dip in the motor battery voltage won't affect the voltage the MCU sees.
2: take the motor voltage directly from the batery but the MCU supply via a diode, followed by a largish bypass cap, say 100 uF off the cuff. The cap will supply the MCU during the dip, and the diode will preven the motor from sucking the cap dry. Of course the diode will cause a ~.7 V drop so make sure you have margin to the minimum MCU supply voltage.