In my physical therapy career, I've had the great privilege to work with athletes across
the spectrum from healthy and able bodied to kids that have suffered severe traumatic injuries that have forever changed their life paths to US National, Olympic and Paralympic athletes (*I'm on the far right in the photo). In my current practice, I generally treat those that are able bodied and have been fortunate to have avoided the pain and trauma that injury and congenital conditions can entail.
The beautiful thing (that can also be very challenging) when working with young athletes is that they are often fortunate enough to have not experienced real pain in their lives. Sure they may have fallen off a bike or got the wind knocked out of them while playing, but generally speaking, healthy kids don't know about pain.
As a result, the aches and pains that arise with being a more specified athlete might surprise them, and finding the words to describe what they are experiencing might be a challenge.
Athletes will experience increased soreness related to an increase in frequency, intensity or duration of their training - think of the transition from a summer swim team to a high school sport. Summer swimmers have a general requirement of 3 practices a week for 1.5-2 hours. Most high school programs have doubles at least a couple days a week and are lifting - this might total 3-5 hours in the pool 6 days a week in addition to time in the weight room. As long as a ramp up occurs and the loads that the athletes are experiencing are progressively increased, the soreness associated with this is expected; that general soreness that is hard to pin point (especially if it's on both sides)? Not usually a big deal.
Generalized soreness related to a new program or exercises might last for 24-36 hours after the exercise, but should not impair one's ability to participate in regular life activities. Yes, going up and down stairs might be hard after a heavy leg day, or putting mascara on after a big shoulder workout might be a challenge, but a specific event can be correlated to this kind of soreness.
However, if an athlete starts complaining of a more specific pain and they can take one or two fingers and pin point where it is, that might start to be a problem. These kinds of issues can usually be narrowed down to a problem with mechanics and are much easier to address in an acute phase versus if the discomfort has been present for a long time. Additionally, when the discomfort is over a specific joint space, tendon or ligament versus a large muscle belly, it's more often something that might require some treatment other than a typical stretch post workout.
Still a little unclear about what you might be able to push through? Try to describe what you're experiencing. As a PT that's worked with a Sports and Performance population for 10+ years, I am rarely surprised by how athletes describe their pain. Words like: dull, aching, sore, gnawing are usually related to more muscular or chronic conditions that can be treated and managed well with strengthening, stabilization and progressive overload. 'Sharp,' 'knife-like,' 'lightning' or 'throbbing' or certainly and description of numbness or tingling would give a provider a little pause with some follow up questions so they can better understand which tissues might be implicated.
A good rule of thumb is to use a pain scale that is subjective just to you - some soreness that doesn't get above a 4/10 is generally ok. If your pain gets higher than that and lasts after whatever activity you're doing, or for sure if you're having a hard time getting to sleep and staying asleep due to your pain, get that checked out sooner than later. Just resting, taking anti-inflammatories and icing what hurts might take away the inflammation that is causing some pain, but won't fix the root cause of why you're having pain in the first place. The sooner you get these things addressed, the sooner you get back to doing what you love to do!