If it's persistent or really bothering you, it's better to err on the side of caution. I'm still reeling from a muscle injury that never felt acute but probably got worse because I just ignored it and kept riding.

I have knee pain frequently, but I don't worry about it because it doesn't persist and it's never really bad. Midway through a ride it will be hurting and then 20 miles later the pain is gone. It's not there the next day, but then a few days later or maybe a week, it bugs me again. I think in my case my knees are just a little creaky but not really injured. I've had this over several years of riding without it getting any worse.