Bot sends 2 messages at a time

My bot just suddenly started sending 2 messages instead of 1, killall node responds with:
node(9): Operation not permitted node(4046): Operation not permitted node(4058): Operation not permitted
How can I fix this issue?

Can you copy and paste the code of your script?

Your bot responds 2 times to the command because there are two instances, to try to remedy this try to regenerate a token to the Discord Developer page.
Using killall node will not work because it does not have the required permissions which will cause :

$ killall node
node(9): Operation not permitted
node(105): Operation not permitted
node(113): Operation not permitted

Try resetting your token then use that resetted token.