Ok, if you haven't suffered any injuries you know of, this could just be simple misalignment - check your foot positioning in relation to your knee; we want your knees going in alignment with your toes as you enter flexion.

Generally speaking, your foot has a big role to play in your knee ache - so if you're doing lower-body stuff like squats, lunges and leg press, your foot positioning and pressure is important. I wouldn't use running shoes (or any other soft shoes) to squat as this will create unnecessary instability. In the same way, think about the pressure in your feet - ideally we want even pressure throughout your entire foot, so if you're shifting too much into the front of your foot, this might create a lot of stress at the front of your knee.

You may be starting slightly too wide for your anatomy (whatever you're doing), and exposing your knee to valgus stress, which is not ideal! Try to pick movements which allow you a more neutral stance (e.g. leg press in a high stance).

Sounds like terminal flexion is not your friend - I would consider limiting your range of movement during whatever you're doing. For example, doing partial reps on the quad extension, choosing a squat variation that involves less knee flexion (safety bar squat), or bringing your feet down on the leg press.

A great thing to do would be to build range of movement tolerance in your knees - one of the best things to do would be to hit some isometrics, building tolerance to deeper ranges of movement: knee-over-toe wallsits, knee-over-toe split squat hold (3 sets of 30-45 seconds on each knee or both knees).

If this is happening on a leg press or a hack squat, a really neat trick is to reverse band this bad boy

Consider your alignment - ideally we want your knee to be more or less in line with your toes as you bend and straighten your leg.

Generally speaking, your foot has a big role to play in your knee ache - so if you're doing lower-body stuff like squats, lunges and leg press, your foot positioning and pressure is important. I wouldn't use running shoes (or any other soft shoes) to squat as this will create unnecessary instability. In the same way, think about the pressure in your feet - ideally we want even pressure throughout your entire foot, so if you're shifting too much into the front of your foot, this might create a lot of stress at the front of your knee.

Check your form on whatever you're doing - if your knees are caving in, you're exposing your knee to valgus stress, which is not ideal! Try to pick movements which allow you a more neutral stance (e.g. foot aligned with knee, knee aligned with hip).

Sounds like terminal extension is a bit of a problem - have a look at your form during squats and leg presses