I've noticed that most intro physics texts (and professors) use uses differentials, the substitution rule, inverse derivatives, and various other things in ways that are almost certain to confuse the average Calculus I student, such that the calculus in the physics material doesn't "feel the same" to them as the calculus they're used to, and they end up feeling like they're on shaky ground.
Sometimes they even just throw complicated calculus at you without really explaining how to think about it conceptually, nor how to solve problems with it in practice. Like for example very early on a text will throw line integrals at you, but won't explain them in any proper way just as mathematical entities in their own right. Or they tell you that center of mass can calculated via an integration, but they completely neglect to even *mention* that you need to use triple integrals to actually do so. And don't even get me started on how hideously they neglect and abuse surface integrals in undergrad textbook material on Gauss's law. So in the end the student is left feeling like there is a lot of hand-wavey magic going on that they really don't quite understand. And the reason is because their Calculus 1 course didn't actually teach enough of the calculus tricks and notations that you need to know to understand calculus based physics, and the tricks are actually pretty simple if someone presents them to you in a straight up pure-math sort of way without mixing in any of the physics related ideas until you're ready.
So if it is the above sort of things that you're having problems with, then perhaps post about the specific calc-based physics theorems that are confusing you, and I'm sure you'll get great explanatory responses. (Or even PM me whenever you do make such a post, and I'll be sure to chime in with my own explanations; which I not surprisingly happen to think are pretty good).