How is your medication used? Is there an applicator?
I can't find too much on why you can't use it, but this mentions that you can't use it with the applicator (I'm assuming it's a plunger-type thing), so that may be part of it). https://www.canesten.co.uk/en/female/products/canesten-thrush-soft-gel-pessary/
https://www.medicinesinpregnancy.org/Medicine--pregnancy/Clotrimazole/ - this says it's safe during pregnancy, but that you use it with your fingers, rather than the applicator.
Never feel intimidated by a doctor. You're in a partnership with her for your health. If you feel like you can't ask your questions, find another doctor who you are comfortable with. Especially during pregnancy, that's important. Your time is just as important as theirs. :)
We all need to listen to our health care providers but there is mixed information on this. If used in the recommended way, it's ordinarily considered safe from my reading. Yes, insert with your fingers. There is this very tiny patient population in a study that said the use may impact masculinization of male offspring. But it is very vague. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5480178/. Has your doctor offered any further information about this?