I've posted about this before but I noticed today that it's still an issue. On my trophy profile page, any game that has DLC (and where I already have the platinum) has an incorrect percentage. I can only surmise that the points for the platinum are being figured into the number, which is not right.
Here's an example. Look at my profile page: onuosfan's PS3 Trophy Profile - PS3Trophies
Uncharted 3 shows with 100/105 trophies, but 100% completion.
What's really strange is that on my single game trophy card, the completion % is correct at 92%.
So one place is being calculated correctly and the other is not - seems like it should be simple enough to make them match... but then again, I'm not the one that has to do it, so what do I know?