I have script generating a usage notification for users every 2nd morning at 05h55. However I find that the script is running twice although Scheduler is set to run it only once.

Has anyone experience a similar problem?

This is a old Problem with the Scheduler.
I hope Mikrotik fixed this Problem.

show us the rules, before we can rule it out as a bug. maybe it's config issue

The rule we use is quiet simple and YES, very often we see the script running twice at the same moment:

/system scheduler
add comment="" disabled=no interval=1d name=backup on-event=backup start-date=jan/01/1970 start-time=00:00:00

YES, this happen for ages, very randomly and very often.

Have you tried latest version?
There was a problem when interval is set to 1 day script will execute twice. I also had this problem, but few versions ago it was fixed.

Can you send me the script aswell. I looked everywhere for a script like that.thanx