It's not a design flaw. And it's not unusual or limited to XDs for the last round in a high capacity magazine to put a lot of pressure on the extractor and the mag release. People report the same problem with Shields and other pistols. If it is problematic for you, simply load the magazine with 12 instead of 13 and the problem disappears. You're still carrying 13 so I wouldn't sweat it.
99% of the magazines that I use which people report having issues getting fully loaded I do NOT have an issue with. Yeah the last round is a little tough, but it goes in. Uplula makes a mag loader that people really seem to like.