I shoot a .338 WM quite a bit and have also noticed the flattened lead tips on rounds that were in the magazine. It does not seem to have much effect on accuracy at normal hunting ranges. Mostly I shoot the Nosler Partitions in my .338 WM rifles. I have shot the flattened tipped bullets into the same groups as the ones that normal tips, much to my surprise. Just give it a try and see if you can measure any difference.
If it causes you grief you can always switch to a plastic tipped bullet such as the AccuBond. The AccuBond shoots slightly smaller groups in my rifles and the tips are less likely to be deformed by heavy recoil.
On my rifles that are larger than the .338 WM I do crimp the bullets so that they will not be shoved deeper into the cases but do not crimp the .338 WM.