Unfortunately, this is a one of a few documented side effects of having your custom time stamps overlaid on top of the default time stamps. From the documentaion:
If the custom timestamp format is longer than the default and you are using dates in tables, table alignment will be messed up. If the custom format is shorter, things do work as expected.
You could try to shorten your custom format, but other than that, you are probably out of luck. Also, notnote that the dates in your example table do not match your custom format. If you hand typed these dates, note that you can add a timestamp automatically in an org-mode buffer with C-.
(org-time-stamp
).