What is your operating system?
What is your Shotcut version (see Help > About Shotcut)?
Can you repeat the problem? If so, what are the steps?
I am adding all my recorded videos uncut to the timeline and start with the stabilization.
So I set up the stabilize filter to one uncut clip, copy it and paste it to all selected clips in the timeline.
But this is only pastes the filter to the first of the clips!
So I had to do it manually!