I suffer from endo and am on depo provera shot. but still having menses. doctor prescribed me duphaston pills twice daily. yesterday i took duphaston for the first time and this morning i have started bleeding dark brownish blood with small clots?

Having "menses" (defined as post-ovulatory bleeding) is not the same as occasional bleeding while on "depo-provera". Additional progestin effect by "duphaston" and consequent withdrawal bleeding may reflect endometrial degeneration from the increase "wearing off". Your stated age of "46" may also indicate sustained estrogen production and no ovulation, causing bleeding.