[HO455]

It is possible that your replacement seal is slightly over sized and/or the bore it fits in is slightly under sized. Thus when the outer part of the seal (which is harder to compress) gets into the bore it won't go any further in. That old engineering bugaboo "Tolerance Stacking"
If it isn't rubbing anything and the lip is on a nice smooth part of the spindle you should be okay to run it protruding.
If you need to get it in further try starting over, but put the seal in the freezer for 30 minutes before starting and preheat the hub to around 175 to 200 degrees. Then try installing the seal. You have to be quick. The temperature difference will give you a couple thousandths more clearance.
Good luck.