I have spray basted cotton batting with no problems. However, there was one time I ended up with a mess. That was when I forgot to use the technique that has you lay out the sandwich first, then pull back the top (or backing) halfway before spraying. I had sprayed the entire backing, then tried to lay the batting on top. Disaster! I did finally manage to work it out, but it took a lot of time and energy.
There are different ways to spray baste, so I am wondering if the technique you used was not suitable for the cotton batting with scrim (which is considerably heavier and harder to manage -- particularly if you are using a hanging technique -- than Hobbs 80/20).
Edit: I tried hanging for spray basting but found the weight was more than my arms liked to handle, especially since I like to make large quilts. It's better for me to lay the sandwich out flat.