Make sure that the tube has a complete and even coverage of glue - any catch is more likely to break out the wood if the catch happens in an area where there is insufficient glue or no glue at all.
Make sure your tools are super sharp, especially on your final cut - cutting end grain with a blunt tool will leave a roughened effect much more than on side grain, as it will push the fibres out of line rather than cut them.
You might find that sanding will take more effort on end grain, and may never be satisfactory without some help - applying sanding sealer repeatedly as you go will firm up the grain and make the job much easier and much more successful.
Pay extra attention to sealing before applying your final finish - end grain will soak up sanding sealer much more than side grain.
Take a photo of the finished pen - photographing a pen with a cross cut blank is just the same as one with a conventionally cut blank, but we all want to see it nonetheless.