I think most athletes are familiar with good vs bad pain.
Good pain is just soreness, typically DOMS, and not an acute injury that you are aggravating. Good pain also tends to be transitory: it comes up with new exercises or increased load, and then goes away. Also, exercise tends to make it feel better.
Bad pain is sharper and tends to be indicative of a more (or at least potentially more) serious injury. It tends to stick around more and over time it gets worse instead of better.
Joint pain in general is universally a bad thing. You can rule out things like DOMS, and instead rule in things like tendinitis, bursitis, and cartilage problems.
To me it seems like I should give my knees extra days off but I would
hate to break my training routine now when the trainings should be
If you're training right, you'll pretty much have that sentiment (maybe not about your knees) forever. These would be, without a doubt, the hardest things in athletic training:
Pushing when you need to push. This is actually the easiest of the hardest things. When you feel like a gazelle, running is enjoyable and fun. When you feel like a beast, pushing lots of weight is fun.
Taking breaks when you need to. Having to stop pushing, having to throttle yourself back, having to push 60% of your weight while some clown next to you is pushing more than you. Basically this is about keeping your ego in check and having faith in the plan.
Getting back on the horse after injuries, illness, and screw ups.
The truth is that taking a week completely off will mean almost zero towards your progression, and might even help. Conversely, if you're flirting with a real injury, pushing through that week can sideline you for much longer amounts of time where you'll spend weeks (or months) unable to train.