Training when fatigued elevates your injury and illness risk, particularly if it’s a high intensity session. You don’t have to be a slave to the workout plan if your body isn’t firing on all cylinders.
Using the first couple of reps of a multi-set session is a good way of creating a pre-main set to the workout (or you could just introduce a pre-main set). A few efforts at a lower intensity than prescribed to get a feel for what you’re capable of.
Another benefit is you can identify areas of serious muscle tension before you go full gas, so you can have a quick stretch or even change the session entirely to avoid turning that tension into an injury.
Consistent high quality training doesn’t mean every session gets done perfectly. It means you are getting the key sessions done and doing what you have to, to keep moving forwards.