If you do Crossfit, we universally share at least one thing... soreness. At first, it can be debilitating and surprising because your first few WODs are typically cut in half (How can a few minutes of air squats in your first session cause you to seek out wheelchair providers?) My legs were the worst. More than once over the first few months, I wanted to install handicap rails around my toilet. Luckily, I perfected the "1 hand between the legs launch off the toilet press" which mitigated the need. But my arms weren't much better, but since I couldn't lift them the pain wasn't as acute. The worst was shampooing my hair. Who knew rubbing your head against "soap on a rope" could work so well. I looked like a cow scratching his head on a fence post, but I didn't care.
In most workout programs, as you repeat often, you rarely experience the initial soreness again. Not at Crossfit. Even the most fit athletes, there will be WODs driving you so hard, your muscles will notice. Some cycles are worse than others, but the soreness never completely mitigates. In a weird way, I enjoy it. After over a year or Crossfit, if I'm not sore, I think I loafed.
This may sound like a bad way to train. But actually it results from one of Crossfit's basic tenants, "highly varied functional movements". We don't do the same movements everyday. We "SHOCK" the body to get results. This means we challenge it in constantly different ways. The positive effect of this is VERY few repetitive motion injuries. The negative effect is a more constant presence of soreness... but normally in a different spot than last week.
Now, what about injuries. As with any sport, workout, or getting off the couch, injuries happen. We know the spiel that it is usually a result of poor form. Regardless, they happen. How do you know the difference? think if you've been coming a while, deep down you know the difference, but don't want to admit it. The easiest way to tell the difference is the immediacy of the pain. If you are working hard and the "soreness" is immediate (i.e. during the workout or just after), it is 95% more likely to be an injury than soreness. Soreness typically takes 24 to 48 hours to feel painful.
The next best way is probably localization. Soreness is more general over the entire muscle you've expended whereas an injury is typically localized to a tear, rip, or break. If you feel an acute, localized pain, you are likely injured and need to stop.
What if it's neither? There is a condition called rhabdomyolysis we should all be aware of. Basically, it is an extreme breakdown of muscle tissue. It causes damage to the muscle but can also be dangerous to kidneys if enough cells enter the bloodstream. The good news is the condition is preventable in most cases with proper hydration and reasonable restraint when exercising. Genetics can make you more or less susceptible to the condition. Some CrossFitters have experienced it (and it was the main focus of a "anti-CF" article in the NY times 6 years ago). But as I said, as long as you aren't going crazy and drink plenty of water, you are unlikely to experience it.
Crossfit... "making you sore in places you didn't know you had for more than a decade."