Although it happens less frequently with Japanese cards, color differences are and have always been a pretty common occurrence. During the WotC era it was especially noticeable. Take all these Pikachus for example:
If we only look at the actual Base Set cards, you can still see quite a few of color differences on first glance. Some light yellow, some darker yellow, some only darker/lighter border, etc. (ignore the sun-bleached card…)
Sometimes the color differences are very clear (especially the bottom two of the picture below, but even the top two have slight color differences of the purple background):
As mentioned earlier, it doesn’t happen too often on Japanese cards, because they have much better quality control. So as bad as above probably won’t happen for Japanese cards. However, even with Japanese cards there have been noticeable color differences before. Here an example of that, which was posted by @linkdu83 a few months back in this thread:
Just like off-centered cards, miscuts, ink drops, print lines, and such, color differences can always occur, although happens more frequently with English cards than Japanese.
Greetz,
Quuador