Should you knees go past your toes when you bend your knees to squat or lunge? In some cases, no. In some cases, yes. Hear me out...
Most often you hear instructors and fitness professionals give a general cue to avoid letting the toes pass the knee. In a class with a large number of participants the instructor will give the most generic cue to keep every body safe. Stress on your knees is increased greatly with added flexion; especially with added weight/resistance. Which means, its safer to air on the side of caution for the knee joint, to ease off the knee past toe situation. The downside to this cue, is that it adds an exceptional amount of stress to the hip joint. In my professional opinion this cue should be different for each client that comes through the facility doors.
Of course, if you have a client with knee issues you are going to give them cues that alleviate any unnecessary stress on their knees. If you have a client with hip issues, you'll do the same for their hip joints.
Simply put, knees over toes is not bad. In fact, you use this motion in your daily life! When you get up from a chair, climb up the stairs, bend over to pick something up, and even when you sit on the toilet, your knees are likely going past your toes. It is a cue that is used in certain situations to help optimize movement while exercising, but shouldn't be taken over into real life functional movement patterns.
If you're curious about how your anatomy works in a squat or lunge and want to know which positions are best for you - book yourself a one-on-one session! Working privately with an instructor is the best way to create a workout plan that suits your individual anatomy. Private pilates sessions can be done in person or virtually with a certified instructor.