What is your Shotcut version (see Help > About Shotcut)? Is it 32-bit?
20.10.31
Can you repeat the problem? If so, what are the steps?
add videos, use crop filter, crop, tick transparent, add size filter, shrink the size.
croped clips become something else.
I reproduced this, and I have a change that fixes this case and still works in some others, but it broke at least one important one - more than likely others as well. Your use case broke in v20.09 when I fixed two bugs when using multiple Size & Position filters - one of which was a crash bug.
It is very difficult to make changes in this area of the code. Between that change and another one in v20.10 to address image quality, it is very risky to make another big change now to accommodate this use case. Trying to cover every combination of things including interaction with other filters, multiple instances of this same filter, and preview scaling is maddening and nearly impossible to reach 100% coverage.
So, if you have a simple workaround by changing the order of filters, you are going to have to take it. The order of filters has always been meaningful, and now it matters to this use case as well. I will try to keep this issue in mind if another one comes along that is similar or benefits from the same change.