If you're experiencing clumps and clogs at the nipple, it is most likely due to not shaking the bottle hard enough. Try adding a little hot water and shake vigorously for 5-10 seconds to help.
If you’re breastfeeding and you're worried you’ll damage the nutrients in your milk, don’t be. It's a common misconception that shaking breast milk harms the nutrients given there isn’t any published data to support the claim.