Usability and performance (for example when deployed on lower-end customer machines) are two major ones. Admittedly they have been getting better over time.
It's also not uncommon to have sites behave a bit differently when running via Burp, so given it's not open source, it can be hard to diagnose/debug what's going on.
It's also not uncommon to have sites behave a bit differently when running via Burp, so given it's not open source, it can be hard to diagnose/debug what's going on.