The clinic is specifically for work related injuries. If you ask to go to the clinic, then you need to be definite that you're reporting an injury that happened at work. You need to be precise; you need to be able to identify how & when the injury happened / when you first noticed the pain.
ANY TIME you report an injury, you should be prepared for some level of harassment. In the last year or so the company has been cracking down on "frivolous" injury claims; even if you were illegitimately injured at work, you can expect that they'll attempt to convince you (including using intimidation & harassment techniques) the injury did not happen at work. Thus, when you report an injury and explicitly state that you're uncertain as to whether the injury occurred at work or not, you can see why there would be a problem.
No, you won't be in trouble tomorrow. But expect a scolding and expect a target to be on your back for awhile. You could always file for your 3.5, but it will only make the situation worse ... and the company will likely counter that you told them you were injured seriously enough to go to the clinic, so thus they couldn't risk you working. They may even issue you a de facto suspension requesting that you provide a doctor's not clearing you to work. (Not likely, but very possible.)
Best advice: think to yourself when you first noticed your injury, determine if you have a history of that type of pain and then think about where the injury happened. Be prepared to say something like "While I was loading Monday, I experienced a sharp pain in my shoulder and I've continued to experience some discomfort. I've never experienced this type of pain before, and while I can't think of what triggered it, it must've happened at work. Otherwise, I can't think of how else it would've happened. Sorry I wasn't clear yesterday." Maybe they'll let you go to the clinic, maybe they'll send you home (to your doctor) or maybe they'll let you work.
When you do return to work, keep your nose clean. And remember -- any interaction you have with management should always be clear & explicit.