There are many ways to track and measure manufacturing performance. One of the most illuminating is to look at the difference between Planned vs Actual performance. This is often tracked through high level metrics such as Schedule Adherence, but the same type of comparative metrics can be used to look for issues at any level of detail.
As a quick example, operation time for a particular machining operation could be tracked and compared to standards. By tracking these times for each piece produced, standard process control rules can be used to determine when there are issues at the operation.
In fact, any issue on the manufacturing floor can be seen through this lens of expected vs actual. Every quality problem is simply a variance from a standard. Machine downtime causes throughput issues versus the plan. Changeovers are not a problem unless they are taking longer than expected or not performed according to the SOP.
Industry 4.0 / Digital Twin solutions have the capability of tracking the planned or expected performance and comparing actuals to those plans in near real time. Alerts and workflows can the be created to handle exceptions as they arise on the shop floor to reduce negative variations over time.