Let me start off by saying that I really don't care for the phrase "listen to your body" because my body wants to be lazy and eat Reese's cups all day... But if your body is asking you to take a break, listen.
I've always had knee problems, that much is not unusual. Most of the time it's fine, but it'll flare up once every month or two and I'll have to cut back on intensity for a couple days, but it generally heals itself in a day or two. This last time, it didn't. So I decided to not do squats or lunges, to avoid stressing my knee too much - it got worse. So I took a day totally off, right before the weekend (my regular rest days). By Monday it was already improving. I've had to take this entire week off of my knee (did a few upper body strength and mat workouts, but no cardio/standing) because I didn't listen when my knee said it needed a break.
Breaks are important!! Overworking yourself will only hurt you in the long run. Even if you don't feel like you're overworking yourself (like me - no major changes in style or length of workout). Let your body (and mind) heal. You'll end up taking off way more time later if you don't listen now!