Arduino motor and motor driver
The L298 is a very old, obsolete design based on bipolar transistors, which means it has a lot of internal losses.

The energy consumed in those losses shows up as heat.

It also has some degree of overload or overtemperature protection, so what you are observing is an automatic shutdown.  Or perhaps, your motor is causing the battery voltage to sag and resetting your Arduino at which point the sketch resumes after a bootloader delay.  6v is really too low an input voltage to the Arduino's regulator, but too high for direct input without the regulator.

You need to make sure that the current draw of your motors is reasonable, and you likely want to replace the terrible L298 with a more modern, low less FET driver.  You will need to select one rated for the actual current draw of your motor: you should consider not only free rotation of the motor, but the increased current draw if it is mechanically stalled.