how do supervisors determine that a phd student is not doing great?
As a postdoc, I have supervised only Master's students. To determine how they are doing, I typically pay attention to three different aspects:


Ability to learn. Can students learn new skills (experimental or computational techniques)? The more advanced a student is, the more independence I'd expect here.
Understanding of subject matter. Does the student understand how their research fits in the broader research field, and why they are using the techniques they are using? Can the student come up with better ways of answering their research question/come up with a better question to answer/find the good question to ask?
Ability to prioritise. How easily does the student identify and work on the most important sub-question to answer? As a project comes close to being finished, can the student keep up a strong pace to deliver final results as quickly as possible?


I don't have a rule to determine when someone isn't doing good enough - I have never had to make that decision. Probably that decision would come when I find that, despite feedback, someone isn't improving on these aspects as I think they should.